How to dig out single particular gene from assembled contigs

[cewells]

Thanks westerman -- we modified for the new blast+ as below --

1) makeblastdb -in Trinity.fasta -dbtype nucl -parse_seqids -out TrinityBlast -title "All contigs"
2) blastn -query myfile.fa -db TrinityBlast -out myfile.out
3) same
4) blastdbcmd -db TrinityBlast -entry myid > found.fa

[westerman]

Local db. Using the older version of blast (although blast+ is similar):

1) formatdb -i Trinity.fasta -p F -o T
2) blastall -p blastn -d Trinity.fasta -i myfile.fa -o output.blastn
3) manually look at output.blastn to figure out the id of the matching contig
4) fastacmd -d Trinity.fasta -s myid > found.fa

[Daisy-Fu]

Blast of your Trinity contigs against the partial sequence? Should be fast enough and sensitive enough to pick up the contig(s). Or am I missing something obvious here?

Hey, Westerman in Purdue, thank you for you replying.
Are you talking about build a local db or www-blast something like that?

[westerman]

Blast of your Trinity contigs against the partial sequence? Should be fast enough and sensitive enough to pick up the contig(s). Or am I missing something obvious here?

[Daisy-Fu]

Sorry if this question has been asked before. I just did a RNA-seq of a plant parasitic nematode species, and assembled 50,000 contigs by Trinity.
I would like to dig out a full-length sequence of endoglucanase gene, and do some protein structure prediction like that. Partial sequence of this gene was available through previous degenerate PCR. Does anybody know a easy and simple way to do it?
Thanks a lot.