MSF multiple alignment format

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Description

This is the GCG format for multiple sequence alignments, it can be parsed with the Bio::AlignIO::msf module which may have specific options.

Example

PileUp

 MSF:  383  Type: P    Check:  3696   .. 

 Name: ALEU_HORVU oo  Len:  383  Check:  9840  Weight:  34.4
 Name: CATH_HUMAN oo  Len:  383  Check:  7134  Weight:  30.1
 Name: CYS1_DICDI oo  Len:  383  Check:  6722  Weight:  35.4

//


ALEU_HORVU      MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
CATH_HUMAN      ......MWAT LPLLCAGAWL LG........ VPVCGAAELS VNSLEK.... 
CYS1_DICDI      .....MKVIL LFVLAVFTVF VS........ .......SRG IPPEEQ.... 


ALEU_HORVU      ALGRTRHALR FARFAVRYGK SYESAAEVRR RFRIFSESLE EVRSTN.... 
CATH_HUMAN      ........FH FKSWMSKHRK TYS.TEEYHH RLQTFASNWR KINAHN.... 
CYS1_DICDI      ........SQ FLEFQDKFNK KYS.HEEYLE RFEIFKSNLG KIEELNLIAI


ALEU_HORVU      RKGLPYRLGI NRFSDMSWEE FQATRLG.AA QTCSATLAGN HLMRDAAA.. 
CATH_HUMAN      NGNHTFKMAL NQFSDMSFAE IKHKYLWSEP QNCSATKS.. NYLRGTGP.. 
CYS1_DICDI      NHKADTKFGV NKFADLSSDE FKNYYLNNKE AIFTDDLPVA DYLDDEFINS 


ALEU_HORVU      LPETKDWRED G.IVSPVKNQ AHCGSCWTFS TTGALEAAYT QATGKNISLS 
CATH_HUMAN      YPPSVDWRKK GNFVSPVKNQ GACGSCWTFS TTGALESAIA IATGKMLSLA 
CYS1_DICDI      IPTAFDWRTR G.AVTPVKNQ GQCGSCWSFS TTGNVEGQHF ISQNKLVSLS


ALEU_HORVU      EQQLVDCAGG FNNF...... ..GCNGGLPS QAFEYIKYNG GIDTEESYPY 
CATH_HUMAN      EQQLVDCAQD FNNY...... ..GCQGGLPS QAFEYILYNK GIMGEDTYPY 
CYS1_DICDI      EQNLVDCDHE CMEYEGEEAC DEGCNGGLQP NAYNYIIKNG GIQTESSYPY
 

ALEU_HORVU      KGVNGVCHYK AENAAVQVLD SVNITLNAED ELKNAVGLVR PVSVAFQVID 
CATH_HUMAN      QGKDGYCKFQ PGKAIGFVKD VANITIYDEE AMVEAVALYN PVSFAFEVTQ 
CYS1_DICDI      TAETGTQCNF NSANIGAKIS NFTMIPKNET VMAGYIVSTG PLAIAADAVE


ALEU_HORVU      GFRQYKSGVY TSDHCGTTPD DVNHAVLAVG YGVEN..... GVPYWLIKNS 
CATH_HUMAN      DFMMYRTGIY SSTSCHKTPD KVNHAVLAVG YGEKN..... GIPYWIVKNS 
CYS1_DICDI      .WQFYIGGVF DIPCN...PN SLDHGILIVG YSAKNTIFRK NMPYWIVKNS 


ALEU_HORVU      WGADWGDNGY FKMEMGKNMC AIATCASYPV VAA
CATH_HUMAN      WGPQWGMNGY FLIERGKNMC GLAACASYPI PLV
CYS1_DICDI      WGADWGEQGY IYLRRGKNTC GVSNFVSTSI I..
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