MAC version of ClustalW

higgins at ebi.ac.uk higgins at ebi.ac.uk
Wed Mar 20 11:30:38 EST 1996


In article <kjt-2003960748260001 at pm074-20.dialip.mich.net>, kjt at umich.edu (Ken J. Takekoshi) writes:
> 
> 
>    Has anyone had any experience with the Macintosh version of ClustalW? 
> I'm trying to give it a go, but I'm having problems.  I don't understand
> how to load in files that are in FAST format in the MAC architecture.  I
> also don't really understand what the dialog box is for that comes up when
> the programs begins.  Something about choosing input and output
> sources/files.
> 
>    Thanks again.
> 
> 
> Sincerely,
> 
> 
> Ken Takekoshi



Hi Ken:

the "Mac version" of ClustalW is not really a mac version; it is just the same
old program recompiled for macs.   Hence it is a bit cryptic; sorry!!
The initial dialogue is not used for anything much; just ignore it.
To get your sequences in, get them together in 1 file in TEXT or ASCII
format (if you are uusing a word processor for example).  here is an
example in fasta format .... just use a ">" to delimit each sequence:

>HBB_HUMAN
          VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST
          PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP
          ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH

>HBB_HORSE
          VQLSGEEKAA VLALWDKVNE EEVGGEALGR LLVVYPWTQR FFDSFGDLSN
          PGAVMGNPKV KAHGKKVLHS FGEGVHHLDN LKGTFAALSE LHCDKLHVDP
          ENFRLLGNVL VVVLARHFGK DFTPELQASY QKVVAGVANA LAHKYH

>HBA_HUMAN
          VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH
          GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL
          LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R

>HBA_HORSE
          VLSAADKTNV KAAWSKVGGH AGEYGAEALE RMFLGFPTTK TYFPHFDLSH
          GSAQVKAHGK KVGDALTLAV GHLDDLPGAL SNLSDLHAHK LRVDPVNFKL
          LSHCLLSTLA VHLPNDFTPA VHASLDKFLS SVSTVLTSKY R

>MYG_PHYCA
          VLSEGEWQLV LHVWAKVEAD VAGHGQDILI RLFKSHPETL EKFDRFKHLK
          TEAEMKASED LKKHGVTVLT ALGAILKKKG HHEAELKPLA QSHATKHKIP
          IKYLEFISEA IIHVLHSRHP GDFGADAQGA MNKALELFRK DIAAKYKELG
          YQG

>GLB5_PETMA
          PIVDTGSVAP LSAAEKTKIR SAWAPVYSTY ETSGVDILVK FFTSTPAAQE
          FFPKFKGLTT ADQLKKSADV RWHAERIINA VNDAVASMDD TEKMSMKLRD
          LSGKHAKSFQ VDPQYFKVLA AVIADTVAAG DAGFEKLMSM ICILLRSAY

>LGB2_LUPLU
          GALTESQAAL VKSSWEEFNA NIPKHTHRFF ILVLEIAPAA KDLFSFLKGT
          SEVPQNNPEL QAHAGKVFKL VYEAAIQLQV TGVVVTDATL KNLGSVHVSK
          GVADAHFPVV KEAILKTIKE VVGAKWSEEL NSAWTIAYDE LAIVIKKEMN
          DAA

Best of luck,
Des Higgins





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