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mjsull / Easyfig

Development version of Easyfig
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blastp on translated proteins? #26

Closed RvV1979 closed 4 years ago

RvV1979 commented 4 years ago

Hi Mitchell, I am trying to use Easyfig binary to depict syntenic blocks across plant genomes. Given that most genes comprise many introns tblastx across the genome nucleotide sequences does not generate the gene-to-gene alignments that I am aiming for but rather produces many small alignments representing individual exons. Is there a way to generate blastp alignments based on the translated proteins? Thanks for your advice

mjsull commented 4 years ago

Hi,

Not at the moment unfortunately. The only way to do this would be replicating the -outfmt 6 option from BLAST. You could also try increasing the minimum length/identity/evalue of reported BLAST hits in the Image->BLAST menu.

Best,

Mitch

On Fri, 8 Nov 2019 at 20:43, RvV1979 notifications@github.com wrote:

Hi Mitchell, I am trying to use Easyfig binary to depict syntenic blocks across plant genomes. Given that most genes comprise many introns tblastx across the genome nucleotide sequences does not generate the gene-to-gene alignments that I am aiming for but rather produces many small alignments representing individual exons. Is there a way to generate blastp alignments based on the translated proteins? Thanks for your advice

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RvV1979 commented 4 years ago

Thanks for the reply. Changing the minimum length/identity/evalue of reported BLAST hits in the Image->BLAST menu does not give me the results I need. I realize that Easyfig was developed for prokaryote genomics but I think that if you would ever add translated protein blast functionality it would be a great tool for a wide community working on Eukaryote genomes, too. Just a thought :-)

On Mon, Nov 18, 2019 at 8:02 AM mjsull notifications@github.com wrote:

Hi,

Not at the moment unfortunately. The only way to do this would be replicating the -outfmt 6 option from BLAST. You could also try increasing the minimum length/identity/evalue of reported BLAST hits in the Image->BLAST menu.

Best,

Mitch

On Fri, 8 Nov 2019 at 20:43, RvV1979 notifications@github.com wrote:

Hi Mitchell, I am trying to use Easyfig binary to depict syntenic blocks across plant genomes. Given that most genes comprise many introns tblastx across the genome nucleotide sequences does not generate the gene-to-gene alignments that I am aiming for but rather produces many small alignments representing individual exons. Is there a way to generate blastp alignments based on the translated proteins? Thanks for your advice

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