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Old 10-11-2010, 06:42 AM   #1
Dalmi
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Red face How to BLAST a genome against Transcriptome sequence

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
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Old 10-11-2010, 11:04 PM   #2
litc
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Default Extract the gene sequence

I think you can extract the gene sequence, then use blastn to align the transcription.
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Old 10-12-2010, 12:59 AM   #3
Dalmi
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I will work on this..
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Old 10-15-2010, 03:17 AM   #4
NicoBxl
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Default

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 )
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