How to BLAST a genome against Transcriptome sequence

[Dalmi]

Hi All,

I have the transcriptome sequence of a fungus. I am looking for some genes. I plan to search these genes in my transcriptome database. However I am confused how will a gene from a genome sequence BLAST against a transcriptome database.

Please help !
Dalmi

[litc]

Extract the gene sequence

I think you can extract the gene sequence, then use blastn to align the transcription.

[Dalmi]

I will work on this..

[NicoBxl]

here's an example of a blast in command line :

blast2 -i query.fasta -d database -p blastn -o output.txt

you can also use the mRNAs sequences of your fungus in the place of the genome ( I think it's more representative )