Question: Blasting an assembly against a single gene of interest
0
gravatar for AGE
8 months ago by
AGE20
AGE20 wrote:

I have two genome assemblies for one species that is polymorphic with respect to colour and a list of genes of interest.

I want to extract the contigs from each assembly that map to a gene of interest, call it gene X.

The way I was thinking of doing this, is by blasting the each assembly against a database containing only the gene of interest in reptiles (my assembly is a snake genome). My goal is to then align the contigs from each assembly that map to gene X and look for mutations.

I know how to limit the query to just a certain taxon (see below), but I'm not sure how to specify just a single gene or if this is possible.

Any constructive input is highly appreciated!

blastn -db refseq_rna -entrez_query="reptilia[ORGN]" \
  -query contigs.fsa -out hits.out -remote \
  -word_size 11 -gapopen 5 -gapextend 2 \
  -penalty -3 -reward 2 -evalue 0.00001 \
  -num_descriptions 3 -num_alignments 3
ADD COMMENTlink modified 8 months ago by h.mon28k • written 8 months ago by AGE20
1

Do it the other way round (if you are going to use blast locally). Use gene X as query against a database of assemblies.

ADD REPLYlink modified 8 months ago • written 8 months ago by genomax74k
1

Of that's right! I'll try that, thanks!

ADD REPLYlink written 8 months ago by AGE20
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