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