User: apulunuj

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apulunuj0
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Posts by apulunuj

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Substitution Error in pal2nal perl script
... I need some help in understanding how to work, the pal2nal.pl script. The program can be obtained from the website, http://www.bork.embl.de/pal2nal/. Whenever I run the script I get an error message at the line, (the line of interest has a comment beside it). THe error message says 'Substitution l ...
nucleotide seq perl script alignment written 13 hours ago by apulunuj0 • updated 7 hours ago by WouterDeCoster21k
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Comment: C: Question: Converting Blast Results/Output to FASTA format
... The output was captured via a job script from which I ran the blast command. Here is the original script. #!/bin/bash #PBS -N transcriptome_blast #PBS -q tiny12core #PBS -j oe #PBS -m abe #PBS -o com_ortho_para.$PBS_JOBID.txt #PBS -l nodes=1:ppn=12 #PBS -l wall ...
written 7 days ago by apulunuj0 • updated 7 days ago by genomax33k
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Comment: C: Question: Converting Blast Results/Output to FASTA format
... Here is my blast command. makeblastdb -in ref_prot.fasta -dbtype prot blastp -query transcriptome.fasta -db ref_prot.fasta -evalue 1e-50 -outfmt '6 qseqid sseqid sseq' ...
written 7 days ago by apulunuj0
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Comment: C: Question: Converting Blast Results/Output to FASTA format
... Here it is. makeblastdb -in ref_prot.fasta -dbtype prot blastp -query transcriptome.fasta -db ref_prot.fasta -evalue 1e-50 -outfmt '6 qseqid sseqid sseq' ...
written 7 days ago by apulunuj0
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Comment: C: Question: Converting Blast Results/Output to FASTA format
... #! usr/bin/env python import sys infile =open('com_ortho_para.3248444.sched.txt') for line in infile: line = line.split(' ') if (',') in line: new_line = line.split(',') query_id = new_line[0] ...
written 7 days ago by apulunuj0 • updated 7 days ago by genomax33k
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Question: Converting Blast Results/Output to FASTA format
... Hello, I am a graduate student with very little background in bioinformatics, and programming. Currently, I am trying to convert my blast output from a job script I ran on a cluster. The output: Building a new DB, current time: 09/11/2017 21:50:46 New DB name: /scratch/napulu/input_prot ...
python sequence alignment written 7 days ago by apulunuj0 • updated 7 days ago by kashifalikhan00740

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