Tag: psiblast

GENE 320 Practical 6 Advanced BLAST Start with a brief introduction [150 words] and aim of the practical. [5] An Introduction should have relevant information relating to the practical, including at least 2 in-text citations from scientific literature (3 marks). The aim/s should be clearly stated. (2 mark) The aim…

Am I correctly running psiblast (using a PSSM as query)? 1 Hello, I am attempting to execute psiblast using multiple PSSMs as queries against a protein database of a specific strain. I previously conducted a blastP and found some results for my proteins of interest, but they were limited. Therefore,…

Hi, I’m trying to install provean and use it on my local machine. I get the following error. error: BLAST database name is missing. Please edit provean.sh file to add the name. I am configuring provean by this command line: ./configure –prefix=/home/elham123456/linux/provean-1.1.5 PSIBLAST=/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/psiblast BLASTDBCMD=/home/elham123456/linux/provean-1.1.5/ncbi-blast-2.14.0+/bin/blastdbcmd CDHIT=/home/elham123456/linux/provean-1.1.5/cd-hit/bin/cd-hit BLAST_DB=/home/elham123456/linux/provean-1.1.5/nr_sep_2012/nr and it is my…

Provided by: libbio-perl-run-perl_1.7.3-8_all NAME Bio::Tools::Run::StandAloneNCBIBlast – Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast. SYNOPSIS # Do not use directly; see Bio::Tools::Run::StandAloneBlast DESCRIPTION See Bio::Tools::Run::StandAloneBlast FEEDBACK Mailing Lists User feedback is an integral part of the evolution of…

How to get gene from PSIBLAST resuts 1 Hello, I am currently utilizing the local version of PSIBLAST to search for homologous genes by comparing a protein sequence against a protein database. However, I am interested in obtaining the nucleotide sequence from the PSIBLAST results. Although I have access to…

Can the value in the pssm (pssm_acsii generated with psiblast) matrix can be greater than 10? 0 Can the value in the pssm (pssm_acsii generated with psiblast) matrix can be greater than 10? I am reading a paper, and his source code of reading pssm_acsii.txt use only ones place of…

keep getting error with psiblast 1 hello I am trying to calculate the PSSM but I keep getting error , where is the problem in this code ? import os import re def command_pssm(content, output_file,pssm_file): os.system(‘psiblast -in_msa 1ak4.fasta -db allseq.fasta -num_threads 10 -num_iterations 3 -evalue 0.001 -out output_file -out_ascii_pssm PSSM.txt’…