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set noglob; $GCGUTILDIR/gcglsf.pl $GCGUTILDIR/fasta ) This kills the Fasta job.

'fg' and 'bg' should be used with caution, as they interfere with the normal execution of a Fasta job, and in some situations can lead to unexpected results especially if a job is foregrounded or backgrounded more than once. Your job may hang, become unkillable, or leave incomplete files.

When should I use stringsearch?

Stringsearch searches through the specified database for a particular character string. You can choose to search through Definitions (option 'A') or Complete Sequence Annotation (option 'B'). The 'A' option is much faster, but both options have been superceded by GCG's Lookup program, which is faster and has more options.

For example, a search through Swissprot for 'glyceraldehyde' takes 25 seconds with Stringsearch Option A, 22 minutes with Stringsearch Option B, and about half a second with Lookup. Lookup searches can also be more easily tailored for your specific needs -- you can search through mouse sequences only, for example. So in most cases, use Lookup instead of Stringsearch.

How can I get a tfasta output aligned with Pileup?

I have a small region of a protein which contains the residues which have been found to be mutated in patients. I want to check Genbank for all homologous proteins to see if these residues are highly conserved. So I want to do a tfasta run to identify the homologs, and then use Pileup to align them. How can I get the list of sequences from a tfasta output into Pileup?

The tfasta output (or the tblastn output) are not suitable for automatic parsing, so it is difficult to get a list of sequence names from the output that you can pop into Pileup.

However, a better way to do this would be to run a <a href="http://molbio.info.nih.gov/molbio/m</body>