« 05.24 EMBOSSを試す その5 | ココ | 05.25 もうそろそろ梅雨のようで »
2009年5月25日
EMBOSSを試す その6
前回edialignコマンドで出力したマルチプルアライメントのデータのうち、FASTA形式のファイルはshowalignコマンドで別の形式で表示することができます。edialignで出力したFASTA形式のファイルをali.fastaとします。
$ showalign ali.fasta
Display a multiple sequence alignment in pretty format
Output file [ali.showalign]: stdout
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus ---nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
FJ981612 ------------------------------------------------------------
GQ117112 ------------------------------------------------------------
GQ131023 ------------------------------------------------------------
AB013810 TTGTTGAACGCAGCAAAGCTTACAGCAACTGTTACCCTTATGATGTGCCGGATTATGCCT
AB043499 ------------------------------------------------------------
AF144305 GCA---------------------------------------------------------
Consensus ---nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnATGAAgGCAAtACTA
FJ981612 ---------------------------------------------...............
GQ117112 ---------------------------------------------...............
GQ131023 ---------------------------------------------...............
AB013810 CCCTTAGGTCACTAGTTGCCTCATCCGGCACCCTGGAGTTTAACA.....A..TTC.A.T
AB043499 ---------------------------------------------.....A....A....
AF144305 ------------------------------------------------------------
Consensus nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnATGAAgGCAAtACTA130 140 150 160 170 180
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus GTAGTTCTGcTaTaTACnnnnnn--nn----nnnnn------n-n----nATTTgCAaCC
FJ981612 .................---------------------------------..........
GQ117112 .................---------------------------------..........
GQ131023 .................---------------------------------..........
AB013810 .G.C.GGA.TCGCTC.GAATGGAACAAGCTTTGCTTGCAAAAGGAGATCT...AAA.GTT
AB043499 C........T.G.G.G.---------------------------------....A..G.T
AF144305 .GG..ATAATCTGTC.AAATGGAGAAAATAGTGCTTCTTCTTGCAATAGTCAG.CTTGT.
Consensus GTAGTTCTGcTaTaTACnnnnnn--nn----nnnnn------n-n----nATTTgCAaCC190 200 210 220 230 240
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus gCAAATGCAGACACAtTATGTATAGGTTATCATGCGAACAAtTCAACAGACACTGTaGAC
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 T.TTTA.T...TTG.A.TG..TGCACCA..T.AAAT----------------------..
AB043499 A..T...........A..........C..C...........C.....T........T...
AF144305 AA..G..ATC.G---A.T..C..T.....C.....A.....C..G.....GCAG..T...
Consensus gCAAATGCAGACACAtTATGTATAGGTTATCATGCGAACAAtTCAACAGACACTGTaGAC250 260 270 280 290 300
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus ACAGTACTAGAAAAGAAtGTaACAGTaACACACTCTGTtAACCTtCTaGAAGACAagCAt
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 .A.TAT.C..C.CT...C..G..TA.GC..A..AA..AC..-------------------
AB043499 ........T..G.....C..G.....G...........C.....A..T..G....GT..C
AF144305 ...A..A.G........C..T..T..T.....TG.CCAAG..A.A..G...A.G.CA..C
Consensus ACAGTACTAGAAAAGAAtGTaACAGTaACACACTCTGTtAACCTtCTaGAAGACAagCAt310 320 330 340 350 360
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus AACGGGAAACTATGCaAACTAAgAGGgGTAGCCCCAtTgCATTTGGGTAAaTGTAaCATT
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 .....A.........CG.....A...AAC.......C.A..A........T..C.G....
AF144305 ..T.....G..C...G.T....AT..A..GAAG..TC.CAT....A.AG.T....GTG.A
Consensus AACGGGAAACTATGCaAACTAAgAGGgGTAGCCCCAtTgCATTTGGGTAAaTGTAaCATT370 380 390 400 410 420
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus GCTGGcTGGATCCTgGGAAATCCAGAGTGTGAATCACTCTcCACaGcaagcTCATGGTCc
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ..C..A......T.A...........A..C........G.TTT.TAAGGAA........T
AF144305 .....A...C....C.....C..TAT......CGA.T..AT..AT.TGCCGGA......T
Consensus GCTGGcTGGATCCTgGGAAATCCAGAGTGTGAATCACTCTcCACaGcaagcTCATGGTCc430 440 450 460 470 480
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TACATTGTGGAAACAtCtAGTtCAGACAATGGAACgTGTTACCCAGGaGATTTCAtCGAt
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 .......CA......C.A.ACC.TA.A........A...........GT.....GC...C
AF144305 .....A.....G.AGG.C...C...C.....ACCTC...........G.......A...C
Consensus TACATTGTGGAAACAtCtAGTtCAGACAATGGAACgTGTTACCCAGGaGATTTCAtCGAt490 500 510 520 530 540
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TATGAGGAgCTaAGAGAGCAATTGAGCTCAGTgTCATCATTTGAaAGgTTTGAGATATTC
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 -----------------------------------------------A.....C.A...G
AB043499 ........A..G..G.................A........C..G..A.....A......
AF144305 .....A..A..G.A.C.C.T.......AG.ACAAACCAT.....G.AAA..C....CA..
Consensus TATGAGGAgCTaAGAGAGCAATTGAGCTCAGTgTCATCATTTGAaAGgTTTGAGATATTC550 560 570 580 590 600
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus CCCAAGacAAGTTCATGGCCCAATCATGActCgAaCAAAGGtGTaACGGCAGCATGTCCt
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 TA..--------------------------------------------------------
AB043499 ......GAT..C...........C..CACTGTA.C......A..G......T....CT.C
AF144305 .....---......T...T..........TG.CTCATC...G..G.GCT..........A
Consensus CCCAAGacAAGTTCATGGCCCAATCATGActCgAaCAAAGGtGTaACGGCAGCATGTCCt610 620 630 640 650 660
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus CATgcTGGagcAAaaAGCTTcTACAAAAATTTaaTATGGCTagTtAAAAAaggaAaTTCA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ...AA...GAA..GC.....T...........GC.......GACGG.G..GAATGGC.TG
AF144305 T.CCA...GAGGTCCTC...T.T..G....G.GG.......TA.C.....GAAC.G.G..
Consensus CATgcTGGagcAAaaAGCTTcTACAAAAATTTaaTATGGCTagTtAAAAAaggaAaTTCA670 680 690 700 710 720
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TACCCAAAgCTcAGCAAaTCCTACATTAATgAtAAaGGgAAAGAAGTCCTcGTGCTATGG
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 -------------------------------------------------------.T...
AB043499 ........T..G.....G.....TG.A..CA.A..G..A...........T.........
AF144305 .......CAA.A.AG.GGAG.....A....ACC..CCAAG....TC.TT.A..A..G...
Consensus TACCCAAAgCTcAGCAAaTCCTACATTAATgAtAAaGGgAAAGAAGTCCTcGTGCTATGG730 740 750 760 770 780
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus GGcATTCACCATCCaTCTACTAgtGCTGACCAAnn-n-n-nnnnnnnnnnnnnnnnnnnn
FJ981612 .................................---------------------------
GQ117112 .................................---------------------------
GQ131023 .................................---------------------------
AB013810 ..GG.......C..GAG...GGACAG.......ACCAGCCTATATGCTCAAGCATCAGGG
AB043499 ..TG....T..C..G....AC.TG.GG......CGGGCCA--------------------
AF144305 ..G...........TAA.GA.GCG..A..G..GACAAAG---------------------
Consensus GGcATTCACCATCCaTCTACTAgtGCTGACCAAnn-n-n-nnnnnnnnnnnnnnnnnnnn790 800 810 820 830 840
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus nnnnnCAaAGTCTCTATCAgAAtGCAgATGCATATGTTTtTGTgGGGTCATCAAgATAcA
FJ981612 -----.......................................................
GQ117112 -----.......................................................
GQ131023 -----.......................................................
AB013810 AGAGT..C........C..A..GAAGCCAA..A.CTG-----------------------
AB043499 ------------.......T..A.A.A....T.......C...ATT...T...CAT..T.
AF144305 -----------........A..CC..ACCA.T..CA...CC..T..AA......C.CTG.
Consensus nnnnnCAaAGTCTCTATCAgAAtGCAgATGCATATGTTTtTGTgGGGTCATCAAgATAcA850 860 870 880 890 900
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus GCAAGAagTTCAagCCGGAAATAGCAAtAAGACCCAAAGTgAGGGATCAAGAAGGGAGAA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ---------.A.TC...A.T..C.G.TCT......TGG..A....G.GTCTCCA.C....
AB043499 ...GA.GA....CC..A..........A...G........A..A................
AF144305 A.C...GA..GGTT..A........T.CT...........A.AC.GG...AGT..A....
Consensus GCAAGAagTTCAagCCGGAAATAGCAAtAAGACCCAAAGTgAGGGATCAAGAAGGGAGAA910 920 930 940 950 960
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TGAACTAtTACTGGACACTAGTAGAGCCGGGAGACAaAATAAcATTCGAaGCAACTGGAA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 .A.G.ATC..T......A.....A.A..........T.C.TCTGA.TA.CAGC..A..G.
AB043499 .T.....C........T..GC.G..A..C..G....C.....T...T..G....A.....
AF144305 ..G.G.TC.T.......A.TT..A.....AAT..TGCC..C.AT.....GAGT.A.....
Consensus TGAACTAtTACTGGACACTAGTAGAGCCGGGAGACAaAATAAcATTCGAaGCAACTGGAA970 980 990 1000 1010 1020
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus ATCTAgTgGtaCCGaGATATGCATTCGCAATGGaAAGAAAtGcTGGaTCtGGtATTATCA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 .....A.T.CT..TC.GGG.TAC...AA...ACG...TGGGAAAA.C..---A..A..G.
AB043499 .....A.A.CG...T.G..C..T......C..AGT...GGCTT...G..A..A..C....
AF144305 ..T.CA.T.CT..AGA........A.AA...T.TC.AG..A.GG.AC..A.CA.....G.
Consensus ATCTAgTgGtaCCGaGATATGCATTCGCAATGGaAAGAAAtGcTGGaTCtGGtATTATCA1030 1040 1050 1060 1070 1080
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TtTCAGATaCACCAgTccaCGAtTGCAATACaActTGTCAgACACCCAAGGGtGCTATAA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 GG......G....CA.TGG.A.A......T.TGAA..CATC..T..A..T..AAGC..TC
AB043499 .C...A.CG..T..A.GGGT..A..TG.CG.T.AG.....A......C.A..A.......
AF144305 AAAGT..ATTGGA.TATGGTA.C.....C..C.AG.....A..T..A.T...G..G....
Consensus TtTCAGATaCACCAgTccaCGAtTGCAATACaActTGTCAgACACCCAAGGGtGCTATAA1090 1100 1110 1120 1130 1140
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus ACACcAGcCTCCCATTTCAGAATATACAtCCGATCACAATTGGAaAATGTCCAAAATATG
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 C..ATGAAAAA........A...G..A.CAG.......TA...GGCC.....C.G.....
AB043499 ...GT..T.....C..C......G....C..AG.......A...G.G........G....
AF144305 ..T.T..TA.G.....C..C..C.....C..CC....C..C..GG....C..C.......
Consensus ACACcAGcCTCCCATTTCAGAATATACAtCCGATCACAATTGGAaAATGTCCAAAATATG1150 1160 1170 1180 1190 1200
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TaAAAAGcACAAAATTGAGACTGGCcACAGGAtTGAGGAATGTCCCgTCtATTCAATCtn
FJ981612 ...........................................................-
GQ117112 ...........................................................-
GQ131023 ...........................................................-
AB013810 .T..GCAA.AC.CTC...A.T....A.....GA..C.......A----------------
AB043499 .C.GG..T........A..GA...TT......C.A.....C.....A..C........C-
AF144305 .G...TCA.AC.G...AGTC..T..G..T...C.C..A...AC...TCAG.GAG.GAGAA
Consensus TaAAAAGcACAAAATTGAGACTGGCcACAGGAtTGAGGAATGTCCCgTCtATTCAATCtn1210 1220 1230 1240 1250 1260
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus nnnnnnnnnnnAGAGGcCTATTTGGgGCcATtGCcGGTTTcATtGAaGGgGGgTGGacaG
FJ981612 -----------.................................................
GQ117112 -----------.................................................
GQ131023 -----------.................................................
AB013810 ------------------------------------------------------------
AB043499 -----------...----------------------------------------------
AF144305 GAAGAAAAAAG.....A........A..T..A..A.....T..A..G..A..A...CAG.
Consensus nnnnnnnnnnnAGAGGcCTATTTGGgGCcATtGCcGGTTTcATtGAaGGgGGgTGGacaG1270 1280 1290 1300 1310 1320
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus GgATGGTAGATGGaTGGTAcGGtTAtCACCATcaaAATGAGCAGGGGtcaGGATAtGCaG
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .A...........T.....T..G..C......AGC............AGT.....C..T.
Consensus GgATGGTAGATGGaTGGTAcGGtTAtCACCATcaaAATGAGCAGGGGtcaGGATAtGCaG1330 1340 1350 1360 1370 1380
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus CcGACctgaAgagCACaCAgAAtGCcATtGAcGanaTtACtAAcAAaGTaAAtTCtgTtA
FJ981612 ..................................A.........................
GQ117112 ..................................G.........................
GQ131023 ..................................G.........................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .A...AAAG.ATC...T..A..G..A..A..T.GAG.C..C..T..G..C..C..GA.C.
Consensus CcGACctgaAgagCACaCAgAAtGCcATtGAcGanaTtACtAAcAAaGTaAAtTCtgTtA1390 1400 1410 1420 1430 1440
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TTGAaAAgATGAAtACaCAGTTcacaGCaGTaGGtAaaGAgTTcAAccACcTGGAAAaaA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 ....C..A.....C..T.....TGAG..C..T..A.GG..A..T..TA..T......GG.
Consensus TTGAaAAgATGAAtACaCAGTTcacaGCaGTaGGtAaaGAgTTcAAccACcTGGAAAaaA1450 1460 1470 1480 1490 1500
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus GaATAGAGAATTTAAAtAAaaAagTtGAtGAtGGtTTCCTgGAcaTtTGGACTTAcAATG
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .G..............C..GC.GA.G..A..C..A.....A..TG.C........T....
Consensus GaATAGAGAATTTAAAtAAaaAagTtGAtGAtGGtTTCCTgGAcaTtTGGACTTAcAATG1510 1520 1530 1540 1550 1560
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus CcGAACTgtTGGTTCTatTGGAAAATGAaAGAACTtTgGACTacCAcGAtTCAAATGTgA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .T.....TC.......CA..........G......C.A....TT..T..C........C.
Consensus CcGAACTgtTGGTTCTatTGGAAAATGAaAGAACTtTgGACTacCAcGAtTCAAATGTgA1570 1580 1590 1600 1610 1620
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus AGAACtTaTATGAaAAGGTaaGAagcCAGcTaAaaaAcAATGCcAAGGAaaTtGGaAAcG
FJ981612 ............................................................
GQ117112 .............................T..............................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .....C.T.....C.....CC..CTA.....T.GGG.T.....A.....GC.G..T..T.
Consensus AGAACtTaTATGAaAAGGTaaGAagcCAGcTaAaaaAcAATGCcAAGGAaaTtGGaAAcG1630 1640 1650 1660 1670 1680
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus GcTGcTTtGAaTTtTAcCACAAATGcGATAAcacgTGcATGGAAAGTGTcAAAAAtGGgA
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .T..T..C..G..C..T........T.....TGAA..T...........A.....C..A.
Consensus GcTGcTTtGAaTTtTAcCACAAATGcGATAAcacgTGcATGGAAAGTGTcAAAAAtGGgA1690 1700 1710 1720 1730 1740
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus CtTATGACTACCCaaAaTAcTCAGAgGAAGCAAaAtTAAACAGAGAaGAAATAgaTGGgG
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .G...........GC.G..T.....A.......G.C..........G......AG...A.
Consensus CtTATGACTACCCaaAaTAcTCAGAgGAAGCAAaAtTAAACAGAGAaGAAATAgaTGGgG1750 1760 1770 1780 1790 1800
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TAAAncTGGAATCAAcaaGgAtTTACCAgATttTGgCgATcTATTCAACtGTcGCcAGTT
FJ981612 ....A.......................................................
GQ117112 ....G.......................................................
GQ131023 ....G.......................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 ....AT.........TGG.A.C......A..AC..T.A..T........A..G..G....
Consensus TAAAncTGGAATCAAcaaGgAtTTACCAgATttTGgCgATcTATTCAACtGTcGCcAGTT1810 1820 1830 1840 1850 1860
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus CatTgGtACTGGtAgTCtcccTgGggGcaaTcagTTTcTGGATGTGCTCtAATGGgTCtc
FJ981612 ............................................................
GQ117112 ............................................................
GQ131023 ............................................................
AB013810 ------------------------------------------------------------
AB043499 ------------------------------------------------------------
AF144305 .CC.A.C.....C.A..ATGG.A.CT.GTC.ATC...A...........C.....A..GT
Consensus CatTgGtACTGGtAgTCtcccTgGggGcaaTcagTTTcTGGATGTGCTCtAATGGgTCtc1870 1880 1890 1900 1910 1920
----:----|----:----|----:----|----:----|----:----|----:----|
Consensus TACAgTGtAGaATaTGtATTTAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
FJ981612 .......................--------------------------------
GQ117112 .......................--------------------------------
GQ131023 ..........G............--------------------------------
AB013810 -------------------------------------------------------
AB043499 -------------------------------------------------------
AF144305 ....A..C.....T..C......ATTTGTGAGTTCAGATTGTAGTTAAAAACACC
Consensus TACAgTGtAGaATaTGtATTTAAnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
By ただ at 00:49 カテゴリー ; 生命科学
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http://pinmarch.sakura.ne.jp/mt/mt-tb.cgi/1420
