Biopython Local Blast Not producing file
Hello, I am a Computer Science & Molecular Biology Student at MIT. I am currently working on my research project in the Research Laboratory of Electronics and I am trying to solve a problem while...
View ArticleParsin nsq database for blast
Hello, I am trying to use biopython to run the local blast. I created the database for Ecoli strain MG6155 and the output results were in nsq format. Now I want to run the local blast using biopython....
View ArticleWeb BLAST Apache configuration (Error 403)
Hi,I'm trying to run Web Blast 2.2.28+ locally trough Easy PHP Dev Server 13.1 (Apache 2.2, Windows 7), but when I click on search it shows ERROR 403 when I open it within my site or the following...
View ArticleNCBI blast command line align two sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
View Articlebatch BLAST two sequences and output sequence alignment
Dear all,I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.FILE1>gene1_species1 atgcatgc...
View ArticleHow to get conservation of vaccine candidates between hundreds of bacterial...
Hi community,We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about...
View ArticleHelp in StandAloneBlast bioperl
Hi, I am new to bioperl. I have been trying to run blast, I get my blast output, I am not sure, how to use $factory in bioperlI have blast installed and has been added to my PATH variable.use...
View ArticleStrange behaviour of BioPerl's Bio::SearchIO when parsing xml BLAST output
Hello, I've noticed some strange behaviour when parsing BLAST .xml output files (-oufmt 5) using BioPerl's Bio::SearchIO library.I have a simple parser script that looks something like:#!/usr/bin/perl...
View ArticleBiopython Local Blast giving mega blast results
Hello Everyone, I am trying to use the stand alone local blast in python to return back to make the blast results of particular sequences. It works but when I tally my results with the online version...
View Articleblast the sequences obtained from translocations to get their positions
HI I have a file that contains information like this:Gene1 Gene2 sequence FOXP1 ABL1 acacctctcaatgcagctttacagCtctacgtctcctccgagagccgctgtggagagttacgtcgaaatgtc FUS ATF1...
View ArticleHow to make statistics of mismatch and unpairing positions between miRNAs and...
Dear all,i need to make statistics of mismatch and unpaired positions between miRNAs and their targets. What I have done is that I performed patscan and identified miRNA targets using various patterns...
View ArticleBLAST - Formatting output
Hi,I've been using the blastn (version 2.2.28+) standalone tool against a custom formatted genome via:blastn -db BLASTDB -word_size 7 -query input.fa -out filename -perc_identity 100 -outfmt 6...
View ArticleFind mismatch and gap positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleHow to find 50 homolgous sequences but not so close related?
Hi, I'm searching for e.g. 50 sequences in Not redudundat blast database. I want to test program for protein mutation prediction - program tries to estimate if mutation is deleterious or...
View Articlestarting point
I am trying to get into bioinformatics or just trying to get a jist of what is going on. I wanted to see the difference between different methods for gene variation. I looked at blast and installed it...
View ArticleOrganisms that have one gene but not an other
Hi, i am looking for organisms in a clade (here: firmicutes), that have one gene (say A) but lack the other (B). Whille I can easily find organisms that have gene A via BLAST search, I am struggling...
View Articleblastcmd
hI,,,I am trying to extract fasta sequences from a local db using blastcmd command (NCBI BLAST) as follows blastdbcmd -db blastdb/9311 -dbtype prot -entry_batch 93hmmsearchacc.txt -out vivien.fastaFor...
View ArticleComparing BLAST m8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
View ArticleHow can I sort blast output based on e-value?
Hello: I have a blast output with about 50000 sequence list. The problem I have is that I need to sort those results based on the smallest e-value to greater e-value. Could you guys please suggest me...
View ArticleHow to generate a Species Distribution from BLAST XML output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
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