Regarding the question regarding reading sequences in various formats.
The following was posted earlier by Don Gilbert and may be of relevance.
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I've updated the sequence reformatter of mine called ReadSeq. This
program comes as C source code that is suitable for Unix, VMS, MS-DOS, or
other command-line systems.
Readseq reads and writes nucleic/protein sequence in these formats:
Stanford/IG, Genbank, NBRF, EMBL, UWGCG, DNA Strider, Fitch,
Pearson, Zuker, Olsen, Phylip v3.2, Phylip v3.3, and Plain text
Data files may have multiple sequences. Software developers are
encouraged to use these routines rather than devise their own obscure
formats. The pascal version of readseq is now out-of-date.
You can get the full set of readseq source and document files as an ARC
archive file thru anonymous ftp to Iubio.bio.indiana.edu. See directory
[archive.molbio.readseq]. Use binary ftp for getting the readseq.arc file.
-- Don
Don.Gilbert at iubio.bio.indiana.edu
biology dept., indiana univ., bloomington, in 47405, usa
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Cheers,
--bruce roe
--broe at aardvark.ucs.uoknor.edu
