how to remove the repeat genes or get the best hsp mathces

Hi, I have performed a blast following the below code:

blastn_cline=NcbiblastnCommandline(query='CDS_extracted_file.fa',db=output + '/temporary_db',evalue=0.001, gapopen=0,gapextend=2,outfmt=5,out=output +'/blast_file.xml')

I have released that some of the genes are repeating as for example:

gene_690 ['phage transcriptional regulator, AlpA']  gnl|BL_ORD_ID|97 NODE_98_length_17475_cov_21.699114 number_gaps: 0  per_identity: 93.6329588015
gene_690 ['phage transcriptional regulator, AlpA']  gnl|BL_ORD_ID|97 NODE_98_length_17475_cov_21.699114 number_gaps: 0  per_identity: 91.7602996255
gene_690 ['phage transcriptional regulator, AlpA']  gnl|BL_ORD_ID|86 NODE_87_length_35482_cov_21.696409 number_gaps: 0  per_identity: 93.

How I can modify the script so I only get the best one? Thanks

blast gene

• 1,613 views • link

written 9.0 years ago by bio90029 •

"max_hsps" option may work if your wrapper has that option. https://www.ncbi.nlm.nih.gov/books/NBK279675/

• 0 views • link

written 9.0 years ago by fishgolden

0 answers

No answers yet.