438:
that is being scored is whether or not two bases are the same at one position. All matches and mismatches are respectively given the same score (typically +1 or +5 for matches, and -1 or -4 for mismatches). But it is different for proteins. Substitution matrices for amino acids are more complicated and implicitly take into account everything that might affect the frequency with which any amino acid is substituted for another. The objective is to provide a relatively heavy penalty for aligning two residues together if they have a low probability of being homologous (correctly aligned by evolutionary descent). Two major forces drive the amino-acid substitution rates away from uniformity: substitutions occur with the different frequencies, and lessen functionally tolerated than others. Thus, substitutions are selected against.
206:
closely related alignments, and BLOSUM45 is used for more distantly related alignments. The matrices were created by merging (clustering) all sequences that were more similar than a given percentage into one single sequence and then comparing those sequences (that were all more divergent than the given percentage value) only; thus reducing the contribution of closely related sequences. The percentage used was appended to the name, giving BLOSUM80 for example where sequences that were more than 80% identical were clustered.
753:
that the same two amino acids might align by chance. The ratio is then converted to a logarithm and expressed as a log odds score, as for PAM. BLOSUM matrices are usually scaled in half-bit units. A score of zero indicates that the frequency with which a given two amino acids were found aligned in the database was as expected by chance, while a positive score indicates that the alignment was found more often than by chance, and negative score indicates that the alignment was found less often than by chance.
22:
123:
cell, potentially causing the cell — and in extreme cases, the organism — to die. Conversely, the change may allow the cell to continue functioning albeit differently, and the mutation can be passed on to the organism's offspring. If this change does not result in any significant physical disadvantage to the offspring, the possibility exists that this mutation will persist within the population. The possibility also exists that the change in function becomes advantageous.
446:
aligned protein sequence used in calculating them. Every possible identity or substitution is assigned a score based on its observed frequencies in the alignment of related proteins. A positive score is given to the more likely substitutions while a negative score is given to the less likely substitutions.
445:
Scores within a BLOSUM are log-odds scores that measure, in an alignment, the logarithm for the ratio of the likelihood of two amino acids appearing with a biological sense and the likelihood of the same amino acids appearing by chance. The matrices are based on the minimum percentage identity of the
437:
A scoring matrix or a table of values is required for evaluating the significance of a sequence alignment, such as describing the probability of a biologically meaningful amino-acid or nucleotide residue-pair occurring in an alignment. Typically, when two nucleotide sequences are being compared, all
752:
The BLOSUM62 matrix with the amino acids in the table grouped according to the chemistry of the side chain, as in (a). Each value in the matrix is calculated by dividing the frequency of occurrence of the amino acid pair in the BLOCKS database, clustered at the 62% level, divided by the probability
205:
Several sets of BLOSUM matrices exist using different alignment databases, named with numbers. BLOSUM matrices with high numbers are designed for comparing closely related sequences, while those with low numbers are designed for comparing distant related sequences. For example, BLOSUM80 is used for
122:
The functionality of a protein is highly dependent on its structure. Changing a single amino acid in a protein may reduce its ability to carry out this function, or the mutation may even change the function that the protein carries out. Changes like these may severely impact a crucial function in a
783:
A novel input representation has been developed consisting of a combination of sparse encoding, Blosum encoding, and input derived from hidden Markov models. this method predicts T-cell epitopes for the genome of hepatitis C virus and discuss possible applications of the prediction method to guide
222:
Eliminate the sequences that are more than r% identical. There are two ways to eliminate the sequences. It can be done either by removing sequences from the block or just by finding similar sequences and replace them by new sequences which could represent the cluster. Elimination is done to remove
184:
When evaluating a sequence alignment, one would like to know how meaningful it is. This requires a scoring matrix, or a table of values that describes the probability of a biologically meaningful amino-acid or nucleotide residue-pair occurring in an alignment. Scores for each position are obtained
130:
vary greatly by the physical and chemical properties of their side chains. However, these amino acids can be categorised into groups with similar physicochemical properties. Substituting an amino acid with another from the same category is more likely to have a smaller impact on the structure and
231:
A database storing the sequence alignments of the most conserved regions of protein families. These alignments are used to derive the BLOSUM matrices. Only the sequences with a percentage of identity lower than the threshold are used. By using the block, counting the pairs of amino acids in each
134:
Sequence alignment is a fundamental research method for modern biology. The most common sequence alignment for protein is to look for similarity between different sequences in order to infer function or establish evolutionary relationships. This helps researchers better understand the origin and
774:
DNA sequences of HBsAg were obtained from 180 patients, in which 51 were chronic HBV carrier and 129 newly diagnosed patients, and compared with consensus sequences built with 168 HBV sequences imported from GenBank. Literature review and BLOSUM scores were used to define potentially altered
441:
Commonly used substitution matrices include the blocks substitution (BLOSUM) and point accepted mutation (PAM) matrices. Both are based on taking sets of high-confidence alignments of many homologous proteins and assessing the frequencies of all substitutions, but they are computed using
355:
792:
BLOSUM matrices are also used as a scoring matrix when comparing DNA sequences or protein sequences to judge the quality of the alignment. This form of scoring system is utilized by a wide range of alignment software including
110:
in a living organism are contained within its DNA. Throughout the cell's lifetime, this information is transcribed and replicated by cellular mechanisms to produce proteins or to provide instructions for daughter cells during
748:
revealed that the BLOSUM62 used for so many years as a standard is not exactly accurate according to the algorithm described by
Henikoff and Henikoff. Surprisingly, the miscalculated BLOSUM62 improves search performance.
538:
93:
score for each of the 210 possible substitution pairs of the 20 standard amino acids. All BLOSUM matrices are based on observed alignments; they are not extrapolated from comparisons of closely related proteins like the
816:
Since both PAM and BLOSUM are different methods for showing the same scoring information, the two can be compared but due to the very different method of obtaining this score, a PAM100 does not equal a BLOSUM100.
214:
BLOSUM matrices are obtained by using blocks of similar amino acid sequences as data, then applying statistical methods to the data to obtain the similarity scores. Statistical
Methods Steps :
240:
It gives the ratio of the occurrence each amino acid combination in the observed data to the expected value of occurrence of the pair. It is rounded off and used in the substitution matrix.
154:
and
Henikoff introduced BLOSUM (BLOcks SUbstitution Matrix) matrix which led to marked improvements in alignments and in searches using queries from each of the groups of related proteins.
419:
388:
199:
Note: BLOSUM 62 is the default matrix for protein BLAST. Experimentation has shown that the BLOSUM-62 matrix is among the best for detecting most weak protein similarities.
725:
571:
245:
665:
638:
705:
685:
611:
591:
1175:
Campbell NA; Reece JB; Meyers N; Urry LA; Cain ML; Wasserman SA; Minorsky PV; Jackson RB (2009). "The
Structure and Function of Large Biological Molecules".
809:. The two result in the same scoring outcome, but use differing methodologies. BLOSUM looks directly at mutations in motifs of related sequences while PAM's
74:
455:
1664:
1284:
1371:
States DJ.; Gish W.; Altschul SF. (1991). "Improved sensitivity of nucleic acid database searches using application-specific scoring matrices".
119:. At the molecular level, there are regulatory systems that correct most — but not all — of these changes to the DNA before it is replicated.
1458:
Mark P Styczynski; Kyle L Jensen; Isidore
Rigoutsos; Gregory Stephanopoulos (2008). "BLOSUM62 miscalculations improve search performance".
143:. Substitution matrices are utilized in algorithms to calculate the similarity of different sequences of proteins; however, the utility of
429:
The odds for relatedness are calculated from log odd ratio, which are then rounded off to get the substitution matrices BLOSUM matrices.
1084:
Campbell NA; Reece JB; Meyers N; Urry LA; Cain ML; Wasserman SA; Minorsky PV; Jackson RB (2009). "The
Molecular Basis of Inheritance".
929:
PAM1 is the matrix calculated from comparisons of sequences with no more than 1% divergence but corresponds to 99% sequence identity.
150:
Matrix has decreased over time due to the requirement of sequences with a similarity more than 85%. In order to fill in this gap,
766:
BLOSUM scores was used to predict and understand the surface gene variants among hepatitis B virus carriers and T-cell epitopes.
196:
E.g., BLOSUM62 is the matrix built using sequences with less than 62% similarity (sequences with ≥ 62% identity were clustered).
1427:
1781:
1114:
Campbell NA; Reece JB; Meyers N; Urry LA; Cain ML; Wasserman SA; Minorsky PV; Jackson RB (2009). "From Gene to
Protein".
1634:
1298:
948:
Larger numbers in matrices naming scheme denote higher sequence similarity and therefore smaller evolutionary distance.
1184:
1154:
1123:
1093:
1417:
1201:
959:
There are several software packages in different programming languages that allow easy use of Blosum matrices.
1776:
967:
932:
BLOSUM 62 is a matrix calculated from comparisons of sequences with a pairwise identity of no more than 62%.
421:
is the expected probability of such a pair occurring, given the background probabilities of each amino acid.
69:
protein sequences. They are based on local alignments. BLOSUM matrices were first introduced in a paper by
1752:
1557:
975:
1733:
1672:
940:
Based on observed alignments; they are not extrapolated from comparisons of closely related proteins.
805:
In addition to BLOSUM matrices, a previously developed scoring matrix can be used. This is known as a
1457:
393:
362:
1608:
1385:
115:, and the possibility exists that the DNA may be altered during these processes. This is known as a
1506:"Viral and clinical factors associated with surface gene variants among hepatitis B virus carriers"
1558:"Reliable prediction of T‐cell epitopes using neural networks with novel sequence representations"
1443:
992:
806:
147:
144:
95:
66:
1146:
1140:
1380:
350:{\displaystyle LogOddRatio=2\log _{2}{\left({\frac {P\left(O\right)}{P\left(E\right)}}\right)}}
1738:
710:
1278:
794:
546:
1035:
745:
643:
616:
8:
727:
is a scaling factor, set such that the matrix contains easily computable integer values.
167:
54:
1360:. Vol. 5. Washington DC: National Biomedical Research Foundation. pp. 345–352.
1039:
1722:
1585:
1535:
1483:
987:
891:
To compare closely related sequences, BLOSUM matrices with higher numbers are created.
690:
670:
596:
576:
171:
140:
136:
78:
58:
1394:
1261:
1234:
1786:
1771:
1726:
1714:
1590:
1527:
1487:
1475:
1423:
1398:
1266:
1251:
1180:
1150:
1119:
1089:
1063:
1058:
1023:
899:
To compare distantly related proteins, BLOSUM matrices with low numbers are created.
131:
function of a protein than replacement with an amino acid from a different category.
1706:
1580:
1572:
1539:
1517:
1467:
1390:
1256:
1246:
1206:
1053:
1043:
26:
896:
To compare distantly related proteins, PAM matrices with high numbers are created.
888:
To compare closely related sequences, PAM matrices with lower numbers are created.
1756:
1697:
Sean R. Eddy (2004). "Where did the BLOSUM62 alignment score matrix come from?".
1642:
151:
70:
1328:
185:
frequencies of substitutions in blocks of local alignments of protein sequences.
1522:
1505:
107:
34:
1326:
1765:
1402:
1048:
945:
Higher numbers in matrices naming scheme denote larger evolutionary distance.
533:{\displaystyle S_{ij}={\frac {1}{\lambda }}\log {\frac {p_{ij}}{q_{i}q_{j}}}}
112:
25:
The BLOSUM62 matrix, the amino acids have been grouped and coloured based on
21:
1718:
1594:
1531:
1479:
1270:
127:
1743:
1067:
1710:
810:
769:
86:
82:
1471:
85:
in the sequence alignment) and then counted the relative frequencies of
1576:
90:
223:
protein sequences that are more similar than the specified threshold.
29:
classification scheme. Positive and zero values have been highlighted.
1139:
Pal JK, Ghaskadbi SS (2009). "DNA Damage, Repair and
Recombination".
963:
116:
1174:
1113:
1083:
971:
175:
62:
1749:
1118:(8th ed.). Pearson Education Australia. pp. 327–350.
1088:(8th ed.). Pearson Education Australia. pp. 307–325.
449:
To calculate a BLOSUM matrix, the following equation is used:
1235:"Having a BLAST with bioinformatics (and avoiding BLASTphemy)"
89:
and their substitution probabilities. Then, they calculated a
1370:
1179:(8th ed.). Pearson Education Australia. pp. 68–89.
813:
evolutionary information based on closely related sequences.
193:
The matrix built from blocks with less than r% of similarity
1232:
667:
are the background probabilities of finding the amino acids
1021:
872:
226:
905:
778:
1556:
Nielsen M, Lundegaard C, Worning P, et al. (2003).
1555:
1327:
1665:"The art of aligning protein sequences Part 1 Matrices"
921:
Based on global alignments of closely related proteins.
65:. BLOSUM matrices are used to score alignments between
1024:"Amino Acid Substitution Matrices from Protein Blocks"
770:
Surface gene variants among hepatitis B virus carriers
713:
693:
673:
646:
619:
599:
579:
549:
458:
396:
365:
248:
1419:
Handbook of Nature-Inspired And
Innovative Computing
1503:
613:replacing each other in a homologous sequence, and
1299:"BLOSSUM MATRICES: Introduction to BIOINFORMATICS"
1145:(1st ed.). Oxford University Press. pp.
719:
699:
679:
659:
632:
605:
585:
565:
532:
413:
382:
349:
209:
1233:pertsemlidis A.; Fondon JW.3rd (September 2001).
1763:
1415:
1499:
1497:
1109:
1107:
1105:
1079:
1077:
432:
181:Scoring metrics (statistical versus biological)
1609:"The Statistics of Sequence Similarity Scores"
1228:
1226:
1224:
1170:
1168:
1166:
937:Other PAM matrices are extrapolated from PAM1.
756:
106:The genetic instructions of every replicating
1613:National Centre for Biotechnology Information
1373:Methods: A Companion to Methods in Enzymology
390:is the probability of observing the pair and
1696:
1494:
1138:
1102:
1074:
1744:Data files of BLOSUM on the NCBI FTP server
1355:
1283:: CS1 maint: numeric names: authors list (
1221:
1163:
800:
1551:
1549:
1453:
1451:
1017:
1015:
1013:
1011:
1009:
1007:
1584:
1521:
1504:Roque-Afonso AM, Ferey MP, Ly TD (2007).
1384:
1329:"CS#594 - Group 13 (Tools and softwares)"
1260:
1250:
1057:
1047:
1750:Interactive BLOSUM Network Visualization
1409:
784:the process of rational vaccine design.
761:
730:
217:
135:function of genes through the nature of
101:
20:
1546:
1448:
1358:Atlas of Protein Sequence and Structure
1349:
1336:University of Illinois at Chicago - UIC
1004:
873:The relationship between PAM and BLOSUM
227:Calculating Frequency & Probability
1764:
1635:"PAM and BLOSUM Substitution Matrices"
1364:
906:The differences between PAM and BLOSUM
779:Reliable prediction of T-cell epitopes
573:is the probability of two amino acids
81:of protein families (that do not have
1022:Henikoff, S.; Henikoff, J.G. (1992).
741:BLOSUM45: distantly related proteins
126:The 20 amino acids translated by the
73:and Jorja Henikoff. They scanned the
1669:Dai hoc Can Tho - Can Tho University
1632:
1199:
954:
707:in any protein sequence. The factor
1356:Margaret O., Dayhoff (1978). "22".
1202:"Mendelian Ratios and Lethal Genes"
13:
1132:
424:
232:column of the multiple alignment.
14:
1798:
1739:Scoring systems for BLAST at NCBI
1690:
1142:Fundamentals of Molecular Biology
235:
1252:10.1186/gb-2001-2-10-reviews2002
735:BLOSUM80: more related proteins
1657:
1626:
1601:
1437:
787:
414:{\displaystyle P\left(E\right)}
383:{\displaystyle P\left(O\right)}
210:Construction of BLOSUM matrices
1320:
1291:
1193:
166:Blocks Substitution Matrix, a
157:
1:
1395:10.1016/s1046-2023(05)80165-3
1306:UNIVERSITI TEKNOLOGI MALAYSIA
1245:(10): reviews2002.1–2002.10.
998:
433:Score of the BLOSUM matrices
7:
1782:Computational phylogenetics
1177:Biology: Australian Version
1116:Biology: Australian Version
1086:Biology: Australian Version
981:
924:Based on local alignments.
757:Some uses in bioinformatics
10:
1803:
1523:10.1177/135965350701200801
1422:. New York, NY: Springer.
1416:Albert Y. Zomaya (2006).
1049:10.1073/pnas.89.22.10915
801:Comparing PAM and BLOSUM
720:{\displaystyle \lambda }
67:evolutionarily divergent
1755:30 January 2017 at the
993:Point accepted mutation
721:
701:
681:
661:
634:
607:
587:
567:
566:{\displaystyle p_{ij}}
534:
415:
384:
351:
30:
1444:NIH "Scoring Systems"
1200:Lobo, Ingrid (2008).
762:Research applications
731:An example - BLOSUM62
722:
702:
682:
662:
660:{\displaystyle q_{j}}
635:
633:{\displaystyle q_{i}}
608:
588:
568:
535:
416:
385:
352:
218:Eliminating Sequences
102:Biological background
24:
1777:Biochemistry methods
1711:10.1038/nbt0804-1035
1699:Nature Biotechnology
1675:on 11 September 2014
1633:Saud, Omama (2009).
746:Nature Biotechnology
711:
691:
671:
644:
617:
597:
577:
547:
456:
394:
363:
246:
1472:10.1038/nbt0308-274
1040:1992PNAS...8910915H
1034:(22): 10915–10919.
738:BLOSUM62: midrange
442:different methods.
168:substitution matrix
55:substitution matrix
53:atrix) matrix is a
16:Bioinformatics tool
1577:10.1110/ps.0239403
988:Sequence alignment
717:
697:
677:
657:
630:
603:
583:
563:
530:
411:
380:
347:
172:sequence alignment
59:sequence alignment
31:
27:Margaret Dayhoff's
1734:BLOCKS WWW server
1429:978-0-387-40532-2
962:Examples are the
955:Software Packages
952:
951:
903:
902:
870:
869:
700:{\displaystyle j}
680:{\displaystyle i}
606:{\displaystyle j}
586:{\displaystyle i}
528:
483:
340:
79:conserved regions
1794:
1730:
1685:
1684:
1682:
1680:
1671:. Archived from
1661:
1655:
1654:
1652:
1650:
1641:. Archived from
1630:
1624:
1623:
1621:
1619:
1605:
1599:
1598:
1588:
1571:(5): 1007–1017.
1562:
1553:
1544:
1543:
1525:
1516:(8): 1255–1263.
1501:
1492:
1491:
1455:
1446:
1441:
1435:
1433:
1413:
1407:
1406:
1388:
1368:
1362:
1361:
1353:
1347:
1346:
1344:
1342:
1333:
1324:
1318:
1317:
1315:
1313:
1303:
1295:
1289:
1288:
1282:
1274:
1264:
1254:
1230:
1219:
1218:
1216:
1214:
1197:
1191:
1190:
1172:
1161:
1160:
1136:
1130:
1129:
1111:
1100:
1099:
1081:
1072:
1071:
1061:
1051:
1019:
910:
909:
877:
876:
820:
819:
726:
724:
723:
718:
706:
704:
703:
698:
686:
684:
683:
678:
666:
664:
663:
658:
656:
655:
639:
637:
636:
631:
629:
628:
612:
610:
609:
604:
592:
590:
589:
584:
572:
570:
569:
564:
562:
561:
539:
537:
536:
531:
529:
527:
526:
525:
516:
515:
505:
504:
492:
484:
476:
471:
470:
420:
418:
417:
412:
410:
389:
387:
386:
381:
379:
356:
354:
353:
348:
346:
345:
341:
339:
338:
323:
322:
307:
297:
296:
1802:
1801:
1797:
1796:
1795:
1793:
1792:
1791:
1762:
1761:
1757:Wayback Machine
1693:
1688:
1678:
1676:
1663:
1662:
1658:
1648:
1646:
1645:on 9 March 2013
1631:
1627:
1617:
1615:
1607:
1606:
1602:
1565:Protein Science
1560:
1554:
1547:
1502:
1495:
1460:Nat. Biotechnol
1456:
1449:
1442:
1438:
1430:
1414:
1410:
1386:10.1.1.114.8183
1369:
1365:
1354:
1350:
1340:
1338:
1331:
1325:
1321:
1311:
1309:
1301:
1297:
1296:
1292:
1276:
1275:
1231:
1222:
1212:
1210:
1198:
1194:
1187:
1173:
1164:
1157:
1137:
1133:
1126:
1112:
1103:
1096:
1082:
1075:
1020:
1005:
1001:
984:
957:
908:
875:
803:
790:
781:
772:
764:
759:
733:
712:
709:
708:
692:
689:
688:
672:
669:
668:
651:
647:
645:
642:
641:
624:
620:
618:
615:
614:
598:
595:
594:
578:
575:
574:
554:
550:
548:
545:
544:
521:
517:
511:
507:
506:
497:
493:
491:
475:
463:
459:
457:
454:
453:
435:
427:
425:BLOSUM Matrices
400:
395:
392:
391:
369:
364:
361:
360:
328:
324:
312:
308:
306:
302:
301:
292:
288:
247:
244:
243:
238:
229:
220:
212:
160:
104:
75:BLOCKS database
71:Steven Henikoff
17:
12:
11:
5:
1800:
1790:
1789:
1784:
1779:
1774:
1760:
1759:
1747:
1741:
1736:
1731:
1692:
1691:External links
1689:
1687:
1686:
1656:
1625:
1600:
1545:
1493:
1466:(3): 274–275.
1447:
1436:
1428:
1408:
1363:
1348:
1319:
1290:
1239:Genome Biology
1220:
1192:
1185:
1162:
1155:
1131:
1124:
1101:
1094:
1073:
1002:
1000:
997:
996:
995:
990:
983:
980:
956:
953:
950:
949:
946:
942:
941:
938:
934:
933:
930:
926:
925:
922:
918:
917:
914:
907:
904:
901:
900:
897:
893:
892:
889:
885:
884:
881:
874:
871:
868:
867:
864:
860:
859:
856:
852:
851:
848:
844:
843:
840:
836:
835:
832:
828:
827:
824:
802:
799:
789:
786:
780:
777:
775:antigenicity.
771:
768:
763:
760:
758:
755:
744:An article in
732:
729:
716:
696:
676:
654:
650:
627:
623:
602:
582:
560:
557:
553:
541:
540:
524:
520:
514:
510:
503:
500:
496:
490:
487:
482:
479:
474:
469:
466:
462:
434:
431:
426:
423:
409:
406:
403:
399:
378:
375:
372:
368:
344:
337:
334:
331:
327:
321:
318:
315:
311:
305:
300:
295:
291:
287:
284:
281:
278:
275:
272:
269:
266:
263:
260:
257:
254:
251:
237:
236:Log odds ratio
234:
228:
225:
219:
216:
211:
208:
203:
202:
201:
200:
197:
191:
189:
186:
182:
179:
164:
159:
156:
103:
100:
35:bioinformatics
15:
9:
6:
4:
3:
2:
1799:
1788:
1785:
1783:
1780:
1778:
1775:
1773:
1770:
1769:
1767:
1758:
1754:
1751:
1748:
1745:
1742:
1740:
1737:
1735:
1732:
1728:
1724:
1720:
1716:
1712:
1708:
1705:(8): 1035–6.
1704:
1700:
1695:
1694:
1674:
1670:
1666:
1660:
1644:
1640:
1636:
1629:
1614:
1610:
1604:
1596:
1592:
1587:
1582:
1578:
1574:
1570:
1566:
1559:
1552:
1550:
1541:
1537:
1533:
1529:
1524:
1519:
1515:
1511:
1507:
1500:
1498:
1489:
1485:
1481:
1477:
1473:
1469:
1465:
1461:
1454:
1452:
1445:
1440:
1431:
1425:
1421:
1420:
1412:
1404:
1400:
1396:
1392:
1387:
1382:
1378:
1374:
1367:
1359:
1352:
1337:
1330:
1323:
1307:
1300:
1294:
1286:
1280:
1272:
1268:
1263:
1258:
1253:
1248:
1244:
1240:
1236:
1229:
1227:
1225:
1209:
1208:
1203:
1196:
1188:
1186:9781442502215
1182:
1178:
1171:
1169:
1167:
1158:
1156:9780195697810
1152:
1148:
1144:
1143:
1135:
1127:
1125:9781442502215
1121:
1117:
1110:
1108:
1106:
1097:
1095:9781442502215
1091:
1087:
1080:
1078:
1069:
1065:
1060:
1055:
1050:
1045:
1041:
1037:
1033:
1029:
1025:
1018:
1016:
1014:
1012:
1010:
1008:
1003:
994:
991:
989:
986:
985:
979:
977:
973:
969:
965:
960:
947:
944:
943:
939:
936:
935:
931:
928:
927:
923:
920:
919:
915:
912:
911:
898:
895:
894:
890:
887:
886:
882:
879:
878:
865:
862:
861:
857:
854:
853:
849:
846:
845:
841:
838:
837:
833:
830:
829:
825:
822:
821:
818:
814:
812:
808:
798:
796:
785:
776:
767:
754:
750:
747:
742:
739:
736:
728:
714:
694:
674:
652:
648:
625:
621:
600:
580:
558:
555:
551:
522:
518:
512:
508:
501:
498:
494:
488:
485:
480:
477:
472:
467:
464:
460:
452:
451:
450:
447:
443:
439:
430:
422:
407:
404:
401:
397:
376:
373:
370:
366:
357:
342:
335:
332:
329:
325:
319:
316:
313:
309:
303:
298:
293:
289:
285:
282:
279:
276:
273:
270:
267:
264:
261:
258:
255:
252:
249:
241:
233:
224:
215:
207:
198:
195:
194:
192:
190:
187:
183:
180:
177:
173:
169:
165:
162:
161:
155:
153:
149:
146:
142:
138:
132:
129:
124:
120:
118:
114:
113:cell division
109:
99:
97:
92:
88:
84:
80:
76:
72:
68:
64:
60:
56:
52:
48:
44:
40:
36:
28:
23:
19:
1702:
1698:
1677:. Retrieved
1673:the original
1668:
1659:
1647:. Retrieved
1643:the original
1638:
1628:
1616:. Retrieved
1612:
1603:
1568:
1564:
1513:
1510:Antivir Ther
1509:
1463:
1459:
1439:
1418:
1411:
1376:
1372:
1366:
1357:
1351:
1339:. Retrieved
1335:
1322:
1310:. Retrieved
1305:
1293:
1279:cite journal
1242:
1238:
1211:. Retrieved
1205:
1195:
1176:
1141:
1134:
1115:
1085:
1031:
1027:
974:library for
961:
958:
815:
804:
791:
788:Use in BLAST
782:
773:
765:
751:
743:
740:
737:
734:
542:
448:
444:
440:
436:
428:
358:
242:
239:
230:
221:
213:
204:
141:conservation
133:
128:genetic code
125:
121:
105:
96:PAM Matrices
50:
46:
42:
38:
32:
18:
1679:7 September
1341:9 September
1312:9 September
966:module for
811:extrapolate
158:Terminology
87:amino acids
49:bstitution
1766:Categories
1649:20 October
1618:20 October
1213:19 October
999:References
1727:205269887
1488:205266180
1403:1046-2023
1381:CiteSeerX
1379:: 66–70.
970:, or the
866:BLOSUM45
858:BLOSUM50
850:BLOSUM62
842:BLOSUM80
834:BLOSUM90
715:λ
489:
481:λ
299:
170:used for
77:for very
57:used for
1787:Matrices
1772:Genetics
1753:Archived
1719:15286655
1595:12717023
1532:18240865
1480:18327232
1434:page 673
1271:11597340
982:See also
188:BLOSUM r
176:proteins
152:Henikoff
137:homology
117:mutation
91:log-odds
63:proteins
1586:2323871
1540:9822759
1147:187–203
1068:1438297
1036:Bibcode
972:BioJava
916:BLOSUM
883:BLOSUM
826:BLOSUM
145:Dayhoff
1725:
1717:
1593:
1583:
1538:
1530:
1486:
1478:
1426:
1401:
1383:
1308:. 2009
1269:
1262:138974
1259:
1207:Nature
1183:
1153:
1122:
1092:
1066:
1056:
968:Python
964:blosum
863:PAM250
855:PAM200
847:PAM160
839:PAM120
831:PAM100
543:Here,
359:where
163:BLOSUM
39:BLOSUM
37:, the
1723:S2CID
1639:Birec
1561:(PDF)
1536:S2CID
1484:S2CID
1332:(PDF)
1302:(PDF)
1059:50453
795:BLAST
1715:PMID
1681:2014
1651:2013
1620:2013
1591:PMID
1528:PMID
1476:PMID
1424:ISBN
1399:ISSN
1343:2014
1314:2014
1285:link
1267:PMID
1215:2013
1181:ISBN
1151:ISBN
1120:ISBN
1090:ISBN
1064:PMID
1028:PNAS
976:Java
687:and
640:and
593:and
139:and
108:cell
83:gaps
45:cks
1707:doi
1581:PMC
1573:doi
1518:doi
1468:doi
1391:doi
1257:PMC
1247:doi
1054:PMC
1044:doi
913:PAM
880:PAM
823:PAM
807:PAM
486:log
290:log
174:of
148:PAM
61:of
43:BLO
33:In
1768::
1721:.
1713:.
1703:22
1701:.
1667:.
1637:.
1611:.
1589:.
1579:.
1569:12
1567:.
1563:.
1548:^
1534:.
1526:.
1514:12
1512:.
1508:.
1496:^
1482:.
1474:.
1464:26
1462:.
1450:^
1397:.
1389:.
1375:.
1334:.
1304:.
1281:}}
1277:{{
1265:.
1255:.
1241:.
1237:.
1223:^
1204:.
1165:^
1149:.
1104:^
1076:^
1062:.
1052:.
1042:.
1032:89
1030:.
1026:.
1006:^
978:.
797:.
98:.
47:SU
1746:.
1729:.
1709::
1683:.
1653:.
1622:.
1597:.
1575::
1542:.
1520::
1490:.
1470::
1432:.
1405:.
1393::
1377:3
1345:.
1316:.
1287:)
1273:.
1249::
1243:2
1217:.
1189:.
1159:.
1128:.
1098:.
1070:.
1046::
1038::
695:j
675:i
653:j
649:q
626:i
622:q
601:j
581:i
559:j
556:i
552:p
523:j
519:q
513:i
509:q
502:j
499:i
495:p
478:1
473:=
468:j
465:i
461:S
408:)
405:E
402:(
398:P
377:)
374:O
371:(
367:P
343:)
336:)
333:E
330:(
326:P
320:)
317:O
314:(
310:P
304:(
294:2
286:2
283:=
280:o
277:i
274:t
271:a
268:R
265:d
262:d
259:O
256:g
253:o
250:L
178:.
51:M
41:(
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
