243:;LCBO - Prolactin precursor - Bovine ; a sample sequence in FASTA format MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC* >MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA DIDGDGQVNYEEFVQMMTAK* >gi|5524211|gb|AAD44166.1| cytochrome b LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY
1693:
3243:
3255:
274:>SEQUENCE_1 MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
231:(or compatible) terminals which could display 80 or 132 characters per line. Most people preferred the bigger font in 80-character modes and so it became the recommended fashion to use 80 characters or less (often 70) in FASTA lines. Also, the width of a standard printed page is 70 to 80 characters (depending on the font). Hence, 80 characters became the norm.
1545:
performs lossless compression of these files using context modelling and arithmetic encoding. Genozip, a software package for compressing genomic files, uses an extensible context-based model. Benchmarks of FASTA file compression algorithms have been reported by
Hosseini et al. in 2016, and Kryukov et al. in 2020.
234:
The first line in a FASTA file started either with a ">" (greater-than) symbol or, less frequently, a ";" (semicolon) was taken as a comment. Subsequent lines starting with a semicolon would be ignored by software. Since the only comment used was the first, it quickly became used to hold a summary
194:
A sequence begins with a greater-than character (">") followed by a description of the sequence (all in a single line). The lines immediately following the description line are the sequence representation, with one letter per amino acid or nucleic acid, and are typically no more than 80 characters
1592:
A plethora of user-friendly scripts are available from the community to perform FASTA file manipulations. Online toolboxes, such as FaBox or the FASTX-Toolkit within Galaxy servers, are also available. These can be used to segregate sequence headers/identifiers, rename them, shorten them, or extract
260:
The description line (defline) or header/identifier line, which begins with ">", gives a name and/or a unique identifier for the sequence, and may also contain additional information. In a deprecated practice, the header line sometimes contained more than one header, separated by a ^A (Control-A)
251:
Modern bioinformatics programs that rely on the FASTA format expect the sequence headers to be preceded by ">". The sequence is generally represented as "interleaved", or on multiple lines as in the above example, but may also be "sequential", or on a single line. Running different bioinformatics
238:
Following the initial line (used for a unique description of the sequence) was the actual sequence itself in the standard one-letter character string. Anything other than a valid character would be ignored (including spaces, tabulators, asterisks, etc...). It was also common to end the sequence with
1593:
sequences of interest from large FASTA files based on a list of wanted identifiers (among other available functions). A tree-based approach to sorting multi-FASTA files (TREE2FASTA) also exists based on the coloring and/or annotation of sequences of interest in the FigTree viewer. Additionally, the
835:
codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap character; and in amino acid sequences, U and * are acceptable letters (see below). Numerical digits are not allowed but are used in some databases to
247:
A multiple-sequence FASTA format, or multi-FASTA format, would be obtained by concatenating several single-sequence FASTA files in one file. This does not imply a contradiction with the format as only the first line in a FASTA file may start with a ";" or ">", forcing all subsequent sequences to
1544:
The compression of FASTA files requires a specific compressor to handle both channels of information: identifiers and sequence. For improved compression results, these are mainly divided into two streams where the compression is made assuming independence. For example, the algorithm MFCompress
287:
defined a standard for the unique identifier used for the sequence (SeqID) in the header line. This allows a sequence that was obtained from a database to be labelled with a reference to its database record. The database identifier format is understood by the NCBI tools like
222:
In the original format, a sequence was represented as a series of lines, each of which was no longer than 120 characters and usually did not exceed 80 characters. This probably was to allow for the preallocation of fixed line sizes in software: at the time most users relied on
3098:
1553:
The encryption of FASTA files can be performed with various tools, including Cryfa and
Genozip. Cryfa uses AES encryption and also enables data compression. Similarly, Genozip can encrypt FASTA files with AES-256 during compression.
235:
description of the sequence, often starting with a unique library accession number, and with time it has become commonplace to always use ">" for the first line and to not use ";" comments (which would otherwise be ignored).
248:
start with a ">" in order to be taken as separate sequences (and further forcing the exclusive reservation of ">" for the sequence definition line). Thus, the examples above would be a multi-FASTA file if taken together.
202:>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA DIDGDGQVNYEEFVQMMTAK*
1607:
Several online format converters exist to rapidly reformat multi-FASTA files to different formats (e.g. NEXUS, PHYLIP) for use with different phylogenetic programs, such as the converter available on phylogeny.fr.
265:
FASTA format, one or more comments, distinguished by a semi-colon at the beginning of the line, may occur after the header. Some databases and bioinformatics applications do not recognize these comments and follow
239:
an "*" (asterisk) character (in analogy with use in PIR formatted sequences) and, for the same reason, to leave a blank line between the description and the sequence. Below are a few sample sequences:
3043:
3007:
2946:
2841:
3025:
219:
suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc, or fastaVN.me—where VN is the
Version Number).
1909:
1871:
3037:
3104:
2575:
Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O (July 2008).
1580:") character. The dots can be discarded for compactness without loss of information. As with typical FASTA files used in alignments, the gap ("
1982:
3051:
2952:
1989:
284:
3080:
1584:") is taken to mean exactly one position. A3M is similar to A2M, with the added rule that gaps aligned to insertions can too be discarded.
3115:
1576:. In A2M/A3M sequences, lowercase characters are taken to mean insertions, which are then indicated in the other sequences as the dot ("
3092:
2224:"Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences"
3086:
2673:
2014:
3074:
2851:
3031:
2929:
2288:
2787:
3286:
3057:
2361:
1452:
for a text file containing FASTA formatted sequences. The table below shows each extension and its respective meaning.
3109:
3013:
2980:
2963:
2923:
1958:
2911:
2899:
3259:
2741:
2495:"TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees"
2442:
Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N, Galaxy Team, Taylor J, Nekrutenko A (2014).
2958:
182:
The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and
2878:
2795:
2763:
2273:
11th
International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB)
224:
3208:
2727:
2666:
1825:
2836:
2759:
2701:
2385:
262:
212:
68:
1770:"The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants"
448:
2816:
2404:
1933:
1565:
is a form of FASTA format extended to indicate information related to sequencing. It is created by the
807:
but are part of the format. Multiple identifiers can be concatenated, also separated by vertical bars.
2545:
681:
2986:
2940:
1993:
1692:
3099:
International
Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
2969:
2305:
1601:
171:
The format allows for sequence names and comments to precede the sequences. It originated from the
3281:
3247:
3213:
2856:
2709:
2659:
51:
3177:
2917:
2705:
3198:
2811:
1632:
formats, used to represent genome sequencer reads that have been aligned to genome sequences.
2275:. Advances in Intelligent Systems and Computing. Vol. 616. Springer. pp. 305–312.
1847:
3182:
1719:
1665:
804:
2271:
Pratas D, Hosseini M, Pinho A (2017). "Cryfa: a tool to compact and encrypt FASTA files".
2032:
8:
3172:
2991:
2779:
2641:
161:
2719:
2018:
1723:
1669:
3228:
3132:
2935:
2601:
2576:
2521:
2494:
2470:
2443:
2338:
2304:
Hosseini, Morteza; Pratas, Diogo; Pinho, Armando J (2019-01-01). Berger, Bonnie (ed.).
2248:
2223:
2158:
2098:
2073:
2050:
1794:
1769:
1656:
Lipman DJ, Pearson WR (March 1985). "Rapid and sensitive protein similarity searches".
1629:
1573:
1449:
824:
296:. The following list describes the NCBI FASTA defined format for sequence identifiers.
252:
programs may require conversions between "sequential" and "interleaved" FASTA formats.
183:
25:
2906:
Microsoft
Research - University of Trento Centre for Computational and Systems Biology
1742:
1707:
3223:
3162:
2737:
2606:
2526:
2475:
2424:
2420:
2343:
2325:
2284:
2253:
2204:
2163:
2145:
2141:
2103:
1865:
1799:
1747:
1681:
1625:
816:
2723:
2321:
2089:
3203:
3167:
2975:
2596:
2588:
2557:
2516:
2506:
2465:
2455:
2416:
2333:
2317:
2276:
2243:
2235:
2194:
2153:
2137:
2093:
2085:
1789:
1781:
1737:
1727:
1673:
2239:
706:
400:
2894:
2280:
2125:
803:
The vertical bars ("|") in the above list are not separators in the sense of the
267:
121:
64:
2561:
815:
Following the header line, the actual sequence is represented. Sequences may be
2682:
1712:
Proceedings of the
National Academy of Sciences of the United States of America
1528:
1360:
548:
176:
145:
86:
2511:
3275:
3157:
2753:
2636:
2428:
2371:
2329:
2208:
2149:
1566:
1401:
1200:
1190:
1180:
1155:
836:
indicate the position in the sequence. The nucleic acid codes supported are:
1677:
3147:
3142:
2631:
2610:
2530:
2479:
2347:
2257:
2167:
2107:
1803:
1732:
1618:
1594:
1562:
832:
820:
149:
110:
1785:
1751:
1685:
2592:
2124:
Lan, Divon; Tobler, Ray; Souilmi, Yassine; Llamas, Bastien (2021-02-15).
1885:
1299:
1279:
1128:
The amino acid codes supported (22 amino acids and 3 special codes) are:
157:
2199:
2182:
3218:
3152:
2771:
2733:
1381:
1289:
1275:
1244:
1230:
1159:
973:
828:
165:
37:
827:). Sequences are expected to be represented in the standard IUB/IUPAC
1405:
1350:
1320:
1220:
1635:
The GVF format (Genome
Variation Format), an extension based on the
2846:
2783:
2775:
2745:
2577:"Phylogeny.fr: robust phylogenetic analysis for the non-specialist"
2460:
2366:
1391:
1330:
1170:
875:
175:
software package and has since become a near-universal standard in
2646:
1621:, used to represent DNA sequencer reads along with quality scores.
823:
sequences, and they can contain gaps or alignment characters (see
2821:
2767:
2715:
2697:
2651:
2441:
1310:
1265:
1240:
1210:
1145:
939:
907:
891:
859:
472:
1817:
731:
424:
3019:
2873:
2826:
2791:
2492:
2183:"A Survey on Data Compression Methods for Biological Sequences"
2074:"MFCompress: a compression tool for FASTA and multi-FASTA data"
1371:
1340:
1255:
991:
956:
923:
2626:
1533:
Contains non-coding RNA regions for a genome, e.g. tRNA, rRNA
2905:
2831:
2493:
Sauvage T, Plouviez S, Schmidt WE, Fredericq S (March 2018).
1008:
228:
216:
172:
100:
96:
3008:
African
Society for Bioinformatics and Computational Biology
2181:
Hosseini, Morteza; Pratas, Diogo; Pinho, Armando J. (2016).
1768:
Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM (April 2010).
756:
633:
2947:
Max Planck
Institute of Molecular Cell Biology and Genetics
2749:
2543:
2444:"Dissemination of scientific software with Galaxy ToolShed"
2221:
1910:"Why is 80 characters the 'standard' limit for code width?"
1636:
164:
or amino acid (protein) sequences, in which nucleotides or
1600:
package can be used to read and manipulate FASTA files in
2574:
2126:"Genozip: a universal extensible genomic data compressor"
1848:"(Now Go Bang!) Raster CRT Typography (According to DEC)"
3026:
International Nucleotide Sequence Database Collaboration
2548:
Biostrings: Efficient manipulation of biological strings
2222:
Kryukov K, Ueda MT, Nakagawa S, Imanishi T (July 2020).
270:. An example of a multiple sequence FASTA file follows:
1572:
A2M/A3M are a family of FASTA-derived formats used for
657:
2544:
Pagès, H; Aboyoun, P; Gentleman, R; DebRoy, S (2018).
2123:
574:(a reference to a database that's not in this list)
2303:
2270:
2180:
1767:
1708:"Improved tools for biological sequence comparison"
2718:, database of protein sequences grouping together
2306:"Cryfa: a secure encryption tool for genomic data"
215:format is described in the documentation for the
3273:
2953:US National Center for Biotechnology Information
31:.fasta, .fas, .fa, .fna, .ffn, .faa, .mpfa, .frn
3038:International Society for Computational Biology
1963:. National Center for Biotechnology Information
3105:ISCB Africa ASBCB Conference on Bioinformatics
2405:"FaBox: an online toolbox for fasta sequences"
1846:Landsteiner, mass:werk, Norbert (2019-02-20).
3052:Institute of Genomics and Integrative Biology
2667:
2037:MAFFT - a multiple sequence alignment program
1990:National Center for Biotechnology Information
1705:
1655:
3081:European Conference on Computational Biology
2435:
1870:: CS1 maint: multiple names: authors list (
3116:Research in Computational Molecular Biology
2071:
1845:
1587:
168:are represented using single-letter codes.
3093:International Conference on Bioinformatics
2674:
2660:
2568:
2486:
2119:
2117:
2065:
1486:Used generically to specify nucleic acids
810:
3087:Intelligent Systems for Molecular Biology
2600:
2520:
2510:
2469:
2459:
2337:
2247:
2198:
2157:
2097:
1793:
1741:
1731:
2402:
16:File format for DNA or protein sequences
3075:Basel Computational Biology Conference‎
2174:
2114:
1980:
1763:
1761:
1699:
3274:
2297:
2264:
3032:International Society for Biocuration
2930:European Molecular Biology Laboratory
2655:
2396:
2362:"Description of A2M alignment format"
1983:"Single Letter Codes for Nucleotides"
1497:Contains coding regions for a genome
1443:
3254:
1758:
1706:Pearson WR, Lipman DJ (April 1988).
1649:
1519:Contains multiple protein sequences
3058:Japanese Society for Bioinformatics
2215:
2072:Pinho AJ, Pratas D (January 2014).
1914:Software Engineering Stack Exchange
313:local (i.e. no database reference)
278:
255:
13:
3020:European Molecular Biology network
2681:
2386:"soedinglab/hh-suite: reformat.pl"
206:
52:Uniform Type Identifier (UTI)
14:
3298:
3110:Pacific Symposium on Biocomputing
3014:Australia Bioinformatics Resource
2981:Swiss Institute of Bioinformatics
2964:Netherlands Bioinformatics Centre
2924:European Bioinformatics Institute
2620:
1494:FASTA nucleotide of gene regions
1092:neither T nor U (i.e. A, C or G)
3253:
3242:
3241:
2912:Database Center for Life Science
2900:Computational Biology Department
2788:Arabidopsis Information Resource
2421:10.1111/j.1471-8286.2007.01821.x
1691:
796:tr|Q90RT2|Q90RT2_9HIV1
2758:Specialised genomic databases:
2537:
2378:
2354:
2043:
2025:
2017:. NIAS DNA Bank. Archived from
2007:
1974:
1852:Now Go Bang! — mass:werk / Blog
1828:from the original on 2022-12-04
542:pgp|EP|0238993|7
516:pat|US|RE33188|1
43:
2959:Japanese Institute of Genetics
2142:10.1093/bioinformatics/btab102
1951:
1926:
1902:
1878:
1839:
1810:
1539:
1508:Contains amino acid sequences
490:sp|P01013|OVAX_CHICK
1:
2879:Rosalind (education platform)
2796:Zebrafish Information Network
2764:Saccharomyces Genome Database
2322:10.1093/bioinformatics/bty645
2090:10.1093/bioinformatics/btt594
1643:
1557:
1548:
1438:
225:Digital Equipment Corporation
3209:List of biological databases
2728:Protein Information Resource
2587:(Web Server issue): W465–9.
2556:. R package version 2.48.0.
2281:10.1007/978-3-319-60816-7_37
1432:gap of indeterminate length
1120:gap of indeterminate length
615:GenInfo integrated database
418:gb|M73307|AGMA13GT
268:the NCBI FASTA specification
7:
2702:European Nucleotide Archive
2562:10.18129/B9.bioc.Biostrings
2240:10.1093/gigascience/giaa072
1611:
1078:not G (i.e., A, C, T or U)
261:character. In the original
189:
10:
3303:
3287:Biological sequence format
1064:not C (i.e. A, G, T or U)
1050:not A (i.e. C, G, T or U)
572:general database reference
566:ref|NM_010450.1|
3237:
3191:
3125:
3067:
3000:
2987:Wellcome Sanger Institute
2941:J. Craig Venter Institute
2887:
2865:
2804:
2689:
2512:10.1186/s13104-018-3268-y
651:dbj|BAC85684.1|
442:emb|CAM43271.1|
364:GenInfo backbone moltype
116:
106:
92:
82:
74:
60:
50:
36:
24:
2970:Philippine Genome Center
1588:Working with FASTA files
603:gnl|taxon|9606
272:
241:
200:
160:for representing either
38:Internet media type
3214:Molecular phylogenetics
2710:China National GeneBank
2409:Molecular Ecology Notes
2051:"Alignment Fileformats"
1934:"FASTA Database Format"
1886:"VT220 Built-in Glyphs"
1818:"What is FASTA format?"
1678:10.1126/science.2983426
1475:Any generic FASTA file
811:Sequence representation
774:tpd|FAA00017|
749:tpe|BN000123|
724:tpg|BK003456|
675:prf||0806162C
608:gnl|PID|e1632
346:GenInfo backbone seqid
2918:DNA Data Bank of Japan
2706:DNA Data Bank of Japan
2581:Nucleic Acids Research
1981:Tao Tao (2011-08-24).
1774:Nucleic Acids Research
1733:10.1073/pnas.85.8.2444
3199:Computational biology
2714:Secondary databases:
2403:Villesen, P. (2007).
1960:NCBI C++ Toolkit Book
1448:There is no standard
466:pir||G36364
2696:Sequence databases:
699:pdb|1I4L|D
162:nucleotide sequences
2992:Whitehead Institute
2780:Rat Genome Database
2392:. 20 November 2022.
2200:10.3390/info7040056
1786:10.1093/nar/gkp1137
1724:1988PNAS...85.2444P
1670:1985Sci...227.1435L
1574:sequence alignments
1483:FASTA nucleic acid
211:The original FASTA/
184:scripting languages
26:Filename extensions
21:
3229:Sequence alignment
2936:Flatiron Institute
2593:10.1093/nar/gkn180
2499:BMC Research Notes
2015:"IUPAC code table"
1516:FASTA amino acids
1450:filename extension
1444:Filename extension
1028:trong interaction
842:Nucleic Acid Code
825:sequence alignment
532:application-number
382:GenInfo import ID
93:Extended from
69:William R. Pearson
19:
3269:
3268:
3224:Sequence database
2738:Protein Data Bank
2732:Other databases:
2290:978-3-319-60815-0
2136:(16): 2225–2230.
1664:(4693): 1435–41.
1537:
1536:
1505:FASTA amino acid
1436:
1435:
1424:translation stop
1126:
1125:
817:protein sequences
801:
800:
522:pre-grant patent
142:
141:
61:Developed by
3294:
3257:
3256:
3245:
3244:
3204:List of biobanks
3168:Stockholm format
2976:Scripps Research
2676:
2669:
2662:
2653:
2652:
2615:
2614:
2604:
2572:
2566:
2565:
2554:Bioconductor.org
2541:
2535:
2534:
2524:
2514:
2490:
2484:
2483:
2473:
2463:
2439:
2433:
2432:
2400:
2394:
2393:
2382:
2376:
2375:
2370:. Archived from
2358:
2352:
2351:
2341:
2301:
2295:
2294:
2268:
2262:
2261:
2251:
2219:
2213:
2212:
2202:
2178:
2172:
2171:
2161:
2121:
2112:
2111:
2101:
2069:
2063:
2062:
2060:
2058:
2047:
2041:
2040:
2029:
2023:
2022:
2011:
2005:
2004:
2002:
2001:
1992:. Archived from
1978:
1972:
1971:
1969:
1968:
1955:
1949:
1948:
1946:
1945:
1930:
1924:
1923:
1921:
1920:
1906:
1900:
1899:
1897:
1896:
1882:
1876:
1875:
1869:
1861:
1859:
1858:
1843:
1837:
1836:
1834:
1833:
1814:
1808:
1807:
1797:
1765:
1756:
1755:
1745:
1735:
1703:
1697:
1696:
1695:
1689:
1653:
1583:
1579:
1455:
1454:
1134:Amino Acid Code
1131:
1130:
1042:eak interaction
990:bases which are
839:
838:
805:Backus–Naur form
797:
792:
775:
770:
750:
745:
725:
720:
700:
695:
676:
671:
652:
647:
628:
627:gi|21434723
623:
609:
604:
598:
586:
567:
562:
543:
538:
517:
512:
491:
486:
467:
462:
443:
438:
419:
414:
395:
390:
377:
372:
359:
354:
340:
335:
329:
321:
299:
298:
295:
291:
279:NCBI identifiers
256:Description line
156:is a text-based
138:
135:
133:
131:
129:
127:
125:
123:
107:Extended to
45:
22:
18:
3302:
3301:
3297:
3296:
3295:
3293:
3292:
3291:
3272:
3271:
3270:
3265:
3233:
3187:
3121:
3063:
3044:Student Council
2996:
2895:Broad Institute
2883:
2861:
2800:
2685:
2680:
2623:
2618:
2573:
2569:
2542:
2538:
2491:
2487:
2440:
2436:
2401:
2397:
2384:
2383:
2379:
2360:
2359:
2355:
2302:
2298:
2291:
2269:
2265:
2220:
2216:
2179:
2175:
2122:
2115:
2070:
2066:
2056:
2054:
2049:
2048:
2044:
2031:
2030:
2026:
2013:
2012:
2008:
1999:
1997:
1979:
1975:
1966:
1964:
1957:
1956:
1952:
1943:
1941:
1932:
1931:
1927:
1918:
1916:
1908:
1907:
1903:
1894:
1892:
1884:
1883:
1879:
1863:
1862:
1856:
1854:
1844:
1840:
1831:
1829:
1816:
1815:
1811:
1766:
1759:
1704:
1700:
1690:
1654:
1650:
1646:
1614:
1590:
1581:
1577:
1560:
1551:
1542:
1469:fasta, fas, fa
1446:
1441:
945:(non-standard)
813:
795:
783:
773:
761:
748:
736:
723:
711:
698:
686:
674:
662:
650:
638:
626:
618:
607:
605:
602:
589:
587:
577:
573:
565:
553:
541:
536:sequence-number
525:
515:
510:sequence-number
499:
489:
477:
465:
453:
441:
429:
417:
405:
393:
385:
375:
367:
357:
349:
339:lcl|hmm271
338:
336:
333:
324:
322:
316:
293:
289:
281:
276:
275:
258:
245:
244:
209:
207:Original format
204:
203:
192:
120:
75:Initial release
67:
65:David J. Lipman
46:
32:
17:
12:
11:
5:
3300:
3290:
3289:
3284:
3282:Bioinformatics
3267:
3266:
3264:
3263:
3251:
3238:
3235:
3234:
3232:
3231:
3226:
3221:
3216:
3211:
3206:
3201:
3195:
3193:
3192:Related topics
3189:
3188:
3186:
3185:
3180:
3175:
3170:
3165:
3160:
3155:
3150:
3145:
3140:
3135:
3129:
3127:
3123:
3122:
3120:
3119:
3113:
3107:
3102:
3096:
3090:
3084:
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3071:
3069:
3065:
3064:
3062:
3061:
3055:
3049:
3048:
3047:
3035:
3029:
3023:
3017:
3011:
3004:
3002:
2998:
2997:
2995:
2994:
2989:
2984:
2978:
2973:
2967:
2961:
2956:
2950:
2944:
2938:
2933:
2927:
2921:
2915:
2909:
2903:
2897:
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2889:
2885:
2884:
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2876:
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2867:
2863:
2862:
2860:
2859:
2854:
2849:
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2839:
2834:
2829:
2824:
2819:
2814:
2808:
2806:
2802:
2801:
2799:
2798:
2756:
2730:
2712:
2693:
2691:
2687:
2686:
2683:Bioinformatics
2679:
2678:
2671:
2664:
2656:
2650:
2649:
2644:
2639:
2637:FigTree viewer
2634:
2629:
2622:
2621:External links
2619:
2617:
2616:
2567:
2536:
2485:
2461:10.1186/gb4161
2448:Genome Biology
2434:
2415:(6): 965–968.
2395:
2377:
2374:on 2022-08-15.
2353:
2316:(1): 146–148.
2310:Bioinformatics
2296:
2289:
2263:
2234:(7): giaa072.
2214:
2173:
2130:Bioinformatics
2113:
2078:Bioinformatics
2064:
2042:
2024:
2021:on 2011-08-11.
2006:
1973:
1950:
1925:
1901:
1877:
1838:
1809:
1780:(6): 1767–71.
1757:
1698:
1647:
1645:
1642:
1641:
1640:
1633:
1622:
1613:
1610:
1589:
1586:
1569:in Cambridge.
1559:
1556:
1550:
1547:
1541:
1538:
1535:
1534:
1531:
1529:non-coding RNA
1525:
1521:
1520:
1517:
1514:
1510:
1509:
1506:
1503:
1499:
1498:
1495:
1492:
1488:
1487:
1484:
1481:
1477:
1476:
1473:
1472:generic FASTA
1470:
1466:
1465:
1462:
1459:
1445:
1442:
1440:
1437:
1434:
1433:
1430:
1426:
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1414:
1410:
1409:
1399:
1395:
1394:
1389:
1385:
1384:
1379:
1375:
1374:
1369:
1365:
1364:
1361:Selenocysteine
1358:
1354:
1353:
1348:
1344:
1343:
1338:
1334:
1333:
1328:
1324:
1323:
1318:
1314:
1313:
1308:
1304:
1303:
1297:
1293:
1292:
1287:
1283:
1282:
1273:
1269:
1268:
1263:
1259:
1258:
1253:
1249:
1248:
1238:
1234:
1233:
1228:
1224:
1223:
1218:
1214:
1213:
1208:
1204:
1203:
1198:
1194:
1193:
1188:
1184:
1183:
1178:
1174:
1173:
1168:
1164:
1163:
1153:
1149:
1148:
1143:
1139:
1138:
1135:
1124:
1123:
1121:
1118:
1114:
1113:
1107:
1104:
1100:
1099:
1098:comes after U
1093:
1090:
1086:
1085:
1084:comes after G
1079:
1076:
1072:
1071:
1070:comes after C
1065:
1062:
1058:
1057:
1056:comes after A
1051:
1048:
1044:
1043:
1037:
1034:
1030:
1029:
1023:
1020:
1016:
1015:
1005:
1002:
998:
997:
988:
985:
981:
980:
971:
968:
964:
963:
954:
951:
947:
946:
937:
934:
930:
929:
921:
918:
914:
913:
905:
902:
898:
897:
889:
886:
882:
881:
873:
870:
866:
865:
857:
854:
850:
849:
846:
843:
812:
809:
799:
798:
793:
781:
777:
776:
771:
759:
752:
751:
746:
734:
727:
726:
721:
709:
702:
701:
696:
684:
678:
677:
672:
660:
654:
653:
648:
636:
630:
629:
624:
616:
612:
611:
600:
575:
569:
568:
563:
551:
545:
544:
539:
523:
519:
518:
513:
497:
493:
492:
487:
475:
469:
468:
463:
451:
445:
444:
439:
427:
421:
420:
415:
403:
397:
396:
391:
383:
379:
378:
373:
365:
361:
360:
355:
347:
343:
342:
331:
314:
310:
309:
306:
303:
280:
277:
273:
257:
254:
242:
208:
205:
201:
191:
188:
177:bioinformatics
146:bioinformatics
140:
139:
118:
114:
113:
108:
104:
103:
94:
90:
89:
87:Bioinformatics
84:
83:Type of format
80:
79:
76:
72:
71:
62:
58:
57:
54:
48:
47:
42:
40:
34:
33:
30:
28:
15:
9:
6:
4:
3:
2:
3299:
3288:
3285:
3283:
3280:
3279:
3277:
3262:
3261:
3252:
3250:
3249:
3240:
3239:
3236:
3230:
3227:
3225:
3222:
3220:
3217:
3215:
3212:
3210:
3207:
3205:
3202:
3200:
3197:
3196:
3194:
3190:
3184:
3181:
3179:
3176:
3174:
3171:
3169:
3166:
3164:
3161:
3159:
3158:Pileup format
3156:
3154:
3151:
3149:
3146:
3144:
3141:
3139:
3136:
3134:
3131:
3130:
3128:
3124:
3117:
3114:
3111:
3108:
3106:
3103:
3100:
3097:
3094:
3091:
3088:
3085:
3082:
3079:
3076:
3073:
3072:
3070:
3066:
3059:
3056:
3053:
3050:
3045:
3042:
3041:
3039:
3036:
3033:
3030:
3027:
3024:
3021:
3018:
3015:
3012:
3009:
3006:
3005:
3003:
3001:Organizations
2999:
2993:
2990:
2988:
2985:
2982:
2979:
2977:
2974:
2971:
2968:
2965:
2962:
2960:
2957:
2954:
2951:
2948:
2945:
2942:
2939:
2937:
2934:
2931:
2928:
2925:
2922:
2919:
2916:
2913:
2910:
2907:
2904:
2901:
2898:
2896:
2893:
2892:
2890:
2886:
2880:
2877:
2875:
2871:
2870:
2868:
2864:
2858:
2855:
2853:
2850:
2848:
2845:
2843:
2840:
2838:
2835:
2833:
2830:
2828:
2825:
2823:
2820:
2818:
2815:
2813:
2810:
2809:
2807:
2803:
2797:
2793:
2789:
2785:
2781:
2777:
2773:
2769:
2765:
2761:
2757:
2755:
2754:Gene Ontology
2751:
2747:
2743:
2739:
2735:
2731:
2729:
2725:
2721:
2717:
2713:
2711:
2707:
2703:
2699:
2695:
2694:
2692:
2688:
2684:
2677:
2672:
2670:
2665:
2663:
2658:
2657:
2654:
2648:
2645:
2643:
2640:
2638:
2635:
2633:
2632:FASTX-Toolkit
2630:
2628:
2625:
2624:
2612:
2608:
2603:
2598:
2594:
2590:
2586:
2582:
2578:
2571:
2563:
2559:
2555:
2551:
2549:
2540:
2532:
2528:
2523:
2518:
2513:
2508:
2504:
2500:
2496:
2489:
2481:
2477:
2472:
2467:
2462:
2457:
2453:
2449:
2445:
2438:
2430:
2426:
2422:
2418:
2414:
2410:
2406:
2399:
2391:
2387:
2381:
2373:
2369:
2368:
2363:
2357:
2349:
2345:
2340:
2335:
2331:
2327:
2323:
2319:
2315:
2311:
2307:
2300:
2292:
2286:
2282:
2278:
2274:
2267:
2259:
2255:
2250:
2245:
2241:
2237:
2233:
2229:
2225:
2218:
2210:
2206:
2201:
2196:
2192:
2188:
2184:
2177:
2169:
2165:
2160:
2155:
2151:
2147:
2143:
2139:
2135:
2131:
2127:
2120:
2118:
2109:
2105:
2100:
2095:
2091:
2087:
2083:
2079:
2075:
2068:
2053:. 22 May 2019
2052:
2046:
2038:
2034:
2028:
2020:
2016:
2010:
1996:on 2012-09-14
1995:
1991:
1987:
1984:
1977:
1962:
1961:
1954:
1939:
1935:
1929:
1915:
1911:
1905:
1891:
1887:
1881:
1873:
1867:
1853:
1849:
1842:
1827:
1823:
1819:
1813:
1805:
1801:
1796:
1791:
1787:
1783:
1779:
1775:
1771:
1764:
1762:
1753:
1749:
1744:
1739:
1734:
1729:
1725:
1721:
1718:(8): 2444–8.
1717:
1713:
1709:
1702:
1694:
1687:
1683:
1679:
1675:
1671:
1667:
1663:
1659:
1652:
1648:
1638:
1634:
1631:
1627:
1623:
1620:
1616:
1615:
1609:
1605:
1603:
1599:
1596:
1585:
1575:
1570:
1568:
1567:Sanger Centre
1564:
1555:
1546:
1532:
1530:
1526:
1523:
1522:
1518:
1515:
1512:
1511:
1507:
1504:
1501:
1500:
1496:
1493:
1490:
1489:
1485:
1482:
1479:
1478:
1474:
1471:
1468:
1467:
1463:
1460:
1457:
1456:
1453:
1451:
1431:
1428:
1427:
1423:
1420:
1419:
1415:
1412:
1411:
1407:
1403:
1402:Glutamic acid
1400:
1397:
1396:
1393:
1390:
1387:
1386:
1383:
1380:
1377:
1376:
1373:
1370:
1367:
1366:
1362:
1359:
1356:
1355:
1352:
1349:
1346:
1345:
1342:
1339:
1336:
1335:
1332:
1329:
1326:
1325:
1322:
1319:
1316:
1315:
1312:
1309:
1306:
1305:
1301:
1298:
1295:
1294:
1291:
1288:
1285:
1284:
1281:
1277:
1274:
1271:
1270:
1267:
1264:
1261:
1260:
1257:
1254:
1251:
1250:
1246:
1242:
1239:
1236:
1235:
1232:
1229:
1226:
1225:
1222:
1219:
1216:
1215:
1212:
1209:
1206:
1205:
1202:
1201:Phenylalanine
1199:
1196:
1195:
1192:
1191:Glutamic acid
1189:
1186:
1185:
1182:
1181:Aspartic acid
1179:
1176:
1175:
1172:
1169:
1166:
1165:
1161:
1157:
1156:Aspartic acid
1154:
1151:
1150:
1147:
1144:
1141:
1140:
1136:
1133:
1132:
1129:
1122:
1119:
1116:
1115:
1111:
1108:
1105:
1102:
1101:
1097:
1094:
1091:
1088:
1087:
1083:
1080:
1077:
1074:
1073:
1069:
1066:
1063:
1060:
1059:
1055:
1052:
1049:
1046:
1045:
1041:
1038:
1035:
1032:
1031:
1027:
1024:
1021:
1018:
1017:
1014:
1012:
1006:
1003:
1000:
999:
996:
994:
989:
986:
983:
982:
979:
977:
972:
969:
966:
965:
962:
960:
955:
952:
949:
948:
944:
942:
938:
935:
932:
931:
928:
926:
922:
919:
916:
915:
912:
910:
906:
903:
900:
899:
896:
894:
890:
887:
884:
883:
880:
878:
874:
871:
868:
867:
864:
862:
858:
855:
852:
851:
847:
844:
841:
840:
837:
834:
830:
826:
822:
818:
808:
806:
794:
791:
787:
782:
779:
778:
772:
769:
765:
760:
758:
754:
753:
747:
744:
740:
735:
733:
729:
728:
722:
719:
715:
710:
708:
704:
703:
697:
694:
690:
685:
683:
680:
679:
673:
670:
666:
661:
659:
656:
655:
649:
646:
642:
637:
635:
632:
631:
625:
622:
617:
614:
613:
610:
601:
599:
597:
593:
585:
581:
576:
571:
570:
564:
561:
557:
552:
550:
547:
546:
540:
537:
533:
529:
524:
521:
520:
514:
511:
507:
503:
498:
495:
494:
488:
485:
481:
476:
474:
471:
470:
464:
461:
457:
452:
450:
447:
446:
440:
437:
433:
428:
426:
423:
422:
416:
413:
409:
404:
402:
399:
398:
392:
389:
384:
381:
380:
374:
371:
366:
363:
362:
356:
353:
348:
345:
344:
341:
332:
330:
328:
320:
315:
312:
311:
307:
304:
301:
300:
297:
286:
271:
269:
264:
253:
249:
240:
236:
232:
230:
226:
220:
218:
214:
199:
198:For example:
196:
187:
185:
180:
178:
174:
169:
167:
163:
159:
155:
151:
147:
137:
119:
115:
112:
109:
105:
102:
98:
95:
91:
88:
85:
81:
77:
73:
70:
66:
63:
59:
55:
53:
49:
41:
39:
35:
29:
27:
23:
3258:
3246:
3153:Nexus format
3148:NeXML format
3143:FASTQ format
3138:FASTA format
3137:
3126:File formats
2888:Institutions
2642:Phylogeny.fr
2627:Bioconductor
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150:biochemistry
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111:FASTQ format
44:text/x-fasta
20:FASTA format
3133:CRAM format
3054:(CSIR-IGIB)
2228:GigaScience
2187:Information
2033:"anysymbol"
1938:www.loc.gov
1540:Compression
1300:Pyrrolysine
1280:Start codon
1007:bases with
953:A or G (I)
308:Example(s)
290:makeblastdb
195:in length.
166:amino acids
3276:Categories
3219:Sequencing
3183:GTF format
3178:GFF format
3173:VCF format
3163:SAM format
2926:(EMBL-EBI)
2852:SOAP suite
2772:VectorBase
2734:BioNumbers
2720:Swiss-Prot
2505:(1): 403.
2454:(2): 403.
2000:2012-03-15
1967:2018-12-19
1944:2024-03-15
1919:2024-03-15
1895:2024-03-15
1857:2024-03-15
1832:2022-12-04
1644:References
1598:Biostrings
1558:Extensions
1549:Encryption
1458:Extension
1439:FASTA file
1382:Tryptophan
1290:Asparagine
1276:Methionine
1245:Isoleucine
1231:Isoleucine
1160:Asparagine
1106:A C G T U
1036:A, T or U
1013:ino groups
987:G, T or U
970:C, T or U
829:amino acid
473:SWISS-PROT
305:Format(s)
3046:(ISCB-SC)
3016:(EMBL-AR)
2949:(MPI-CBG)
2690:Databases
2429:1471-8278
2330:1367-4803
2209:2078-2489
2193:(4): 56.
2150:1367-4803
1822:Zhang Lab
1406:Glutamine
1351:Threonine
1321:Glutamine
1221:Histidine
978:rimidines
848:Mnemonic
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3248:Category
3118:(RECOMB)
3068:Meetings
3022:(EMBnet)
2872:Server:
2847:SAMtools
2842:PANGOLIN
2805:Software
2784:PHI-base
2776:WormBase
2746:InterPro
2611:18424797
2531:29506565
2480:25001293
2367:SAMtools
2348:30020420
2258:32627830
2168:33585897
2108:24132931
1866:cite web
1826:Archived
1804:20015970
1612:See also
1461:Meaning
1392:Tyrosine
1331:Arginine
1171:Cysteine
1137:Meaning
845:Meaning
784:tr|
619:gi|
592:database
580:database
478:sp|
406:gb|
190:Overview
3260:Commons
3095:(InCoB)
3040:(ISCB)
3028:(INSDC)
3010:(ASBCB)
2914:(DBCLS)
2908:(COSBI)
2822:Clustal
2768:FlyBase
2742:Ensembl
2716:UniProt
2698:GenBank
2602:2447785
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2339:6298042
2249:7336184
2159:8388020
2099:3866555
1795:2847217
1752:3162770
1720:Bibcode
1686:2983426
1666:Bibcode
1658:Science
1639:format.
1404:(E) or
1363:(rare)
1311:Proline
1302:(rare)
1266:Leucine
1243:(L) or
1241:Leucine
1211:Glycine
1158:(D) or
1146:Alanine
1022:C or G
1004:A or C
879:ytosine
780:TrEMBL
707:GenBank
621:integer
584:integer
528:country
502:country
496:patent
401:GenBank
388:integer
370:integer
352:integer
319:integer
263:Pearson
213:Pearson
117:Website
3101:(CIBB)
3089:(ISMB)
3083:(ECCB)
3060:(JSBi)
2966:(NBIC)
2955:(NCBI)
2943:(JCVI)
2932:(EMBL)
2920:(DDBJ)
2874:ExPASy
2857:TopHat
2837:MUSCLE
2827:EMBOSS
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2792:GISAID
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1464:Notes
1372:Valine
1341:Serine
1256:Lysine
995:etones
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911:hymine
895:uanine
863:denine
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227:(DEC)
158:format
152:, the
136:.shtml
134:/fasta
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3034:(ISB)
2983:(SIB)
2972:(PGC)
2902:(CBD)
2866:Other
2832:HMMER
2812:BLAST
1890:VT100
1513:mpfa
927:racil
693:chain
689:entry
645:locus
436:locus
412:locus
302:Type
229:VT220
217:FASTA
173:FASTA
124:.ncbi
101:FASTA
97:ASCII
2794:and
2760:BOLD
2750:KEGG
2726:and
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2607:PMID
2527:PMID
2476:PMID
2425:ISSN
2344:PMID
2326:ISSN
2285:ISBN
2254:PMID
2205:ISSN
2164:PMID
2146:ISSN
2104:PMID
2059:2019
1872:link
1800:PMID
1748:PMID
1682:PMID
1637:GFF3
1630:CRAM
1628:and
1624:The
1617:The
1524:frn
1502:faa
1491:ffn
1480:fna
1416:any
1408:(Q)
1247:(I)
1162:(N)
933:(i)
831:and
790:name
768:name
757:DDBJ
743:name
732:EMBL
718:name
669:name
634:DDBJ
560:name
484:name
460:name
425:EMBL
292:and
285:NCBI
283:The
148:and
130:.gov
128:.nih
126:.nlm
99:for
78:1985
2647:GTO
2597:PMC
2589:doi
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1738:PMC
1728:doi
1674:doi
1662:227
1626:SAM
961:ine
819:or
682:PDB
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449:PIR
144:In
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