User: adhirajnath14

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Posts by adhirajnath14

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Sliding Window with specific window size and step size in BioPython
... I have multiple sequences in a fasta file and I want to divide it into sliding window with window size 90 and step size 10. I have a python script as follows: from Bio import SeqIO with open("my90_out.txt","w") as f: for seq_record in SeqIO.parse("myseq.fasta", "fasta"): ...
python biopython written 11 hours ago by adhirajnath140
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Comment: C: Extract flanking region of -500 nt upstream and downstream of BLAST result on ge
... Thank you so much. I'll use it and let you know if any problems ...
written 4 days ago by adhirajnath140
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Comment: C: Adding -type arguments of blastn in Bioperl
... Thank you so much. It worked! ...
written 4 days ago by adhirajnath140
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Comment: C: How To Get Sequence Around Blast Result?
... Thank you so much. What if we want to parse 50 nt flanks with the aligned sequence? ...
written 4 days ago by adhirajnath140
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Extract flanking region of -500 nt upstream and downstream of BLAST result on genome using perl scripts
... I have performed BLAST on a set of 380 sequences on a genome using BLAST+. I need to extract the aligned region along with (-/+)500 nt flanks for each hit from the genome. Can anyone provide me a script in perl or guide a way to do it. I know it can be done but have not found any reliable sources. I ...
genome alignment sequence assembly written 6 days ago by adhirajnath140 • updated 6 days ago by jean.elbers1.2k
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Comment: C: Adding -type arguments of blastn in Bioperl
... Sorry about the typo. I didn't copy paste it, that's why. Anyway, it does not work with it. ...
written 6 days ago by adhirajnath140
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Comment: C: How To Get Sequence Around Blast Result?
... What if we have a query with 100 sequences? Manual parsing may not be feasible. ...
written 6 days ago by adhirajnath140
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Comment: C: Adding -type arguments of blastn in Bioperl
... Thank you sir for responding. I tried `$result = $fac->blastn( -query => 'myquery.fasta', -task -> 'blastn-short' -outfile => 'result01.txt', -outformat => 9)` It does not work. ...
written 6 days ago by adhirajnath140
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Adding -type arguments of blastn in Bioperl
... I need to run a blast for small query sequence in bioperl. The way to do it in blast standalone program is by adding ./blastn -db nt -remote -query test2.seq -task "blastn-short" -out test2.out Is there a way to add -task arguments in BioPerl? Thank you ...
alignment sequence written 7 days ago by adhirajnath140 • updated 7 days ago by JC8.2k

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