Stop me if this is stupid!

Bob Friedman friedmar at biol.sc.edu
Mon Jun 19 10:41:21 EST 2000


"Fraggle_Rock"
> I am currently searching some of the exciting new sequence databases for
> psuedogenes, and gene fragments that have becom 'junk' dna in various
> species.

If the gene isn't expressed, you should find stop codons in the coding
region.  Perhaps try a tblastn search (blast) of the nr database.
>
> I am mainly using blast and fasta type programs, picking regions that look
> like they have some homology from 'good' genes, then doing multiple
> alignments (clustalX).

Alignments using the protein or the DNA?
>
> I have been playing around with dotplots also, and they are a very
powerful
> visual way of seeing regions that are abit homologous, but they limit you
> to 2 sequences. I was wondering if there are any programs that let you put
> a multiply aligned set of sequences (or HMM of a set of sequences) down
one
> axis and a query sequecnce along the other, and give some sort of colour
> reperesentation of homology match?

Perhaps finding a concensus sequence for the multiple set and the query on
the other.  Dottup and Dotter programs work well.
>
> cheers
>
> Fragg

Bob








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