[WashU] HMMER
User's Guide


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Subsections

sreformat - convert sequence file to different format

Synopsis

sreformat [options] format seqfile

Description

sreformat reads the sequence file seqfile in any supported format, reformats it into a new format specified by format, then prints the reformatted text.

Supported input formats include (but are not limited to) the unaligned formats FASTA, Genbank, EMBL, SWISS-PROT, PIR, and GCG, and the aligned formats SELEX, Clustal, and GCG MSF.

Available unaligned output file format codes include fasta (FASTA format); embl (EMBL/SWISSPROT format); genbank (Genbank format); gcg (GCG single sequence format); gcgdata (GCG flatfile database format); strider (MacStrider format); zuker (Zuker MFOLD format); ig (Intelligenetics format); pir (PIR/CODATA flatfile format); squid (an undocumented St. Louis format); raw (raw sequence, no other information). The available aligned output file format codes include selex (SELEX/HMMER/Pfam annotated alignment format); msf (GCG MSF format); and a2m (aligned FASTA format, called A2M by the UC Santa Cruz HMM group).

Unaligned format files cannot be reformatted to aligned formats. However, aligned formats can be reformatted to unaligned formats - gap characters are simply stripped out.

This program was originally named reformat, but that name clashes with a GCG program of the same name.

Options

Expert Options


next up previous contents
Next: File formats Up: Manual pages Previous: seqstat - show statistics


Direct comments and questions to <eddy@genetics.wustl.edu>