How To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View ArticleHow to use whole computer cluster power for computation of a single job?
I know the computations by breaking the files and parallelize it in SGE or SLURM. I want to use whole computation power (20 node , 80 cores) for a single job without breaking it. If I just submit it (a...
View ArticleIndividual Hit Gene Information From Qblast Xml Output
I've just started using Biopython, and I am trying to perform remote BLAST operations using the qblast() function. Everything seems to be working properly, but I am not being able to retrieve an...
View ArticleRunning Blast For A List Of Pairs
Hi,I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?I tried bl2seq but unfortunately it does not produce the alignment of the whole...
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
View ArticleBLASTP many pairs of peptide sequences
Dear all,I have many pairs of protein sequences, an example shown below.MDDDIAALVVDNGSGMCKAGÂ DDDIAALVDNSGSMCKAGTTAEREIVRDIKEKLCYÂ TTAEIVRKEKLCYVARMQKEITAPSTMKIKIÂ KEITALPSTMKIKII... ...I need to...
View ArticleRunning A Standalone Batch Blast With Fasta File Using Perl, Can'T Get...
I'm running standalone blast locally. My blast query sequencess are in a fasta file called human_seqs.fasta, which comprise around 300 sequences. Being blasted against a much larger database called...
View ArticleMethod Of Getting Progress Of A Blast Run
Are there any parameters in blastall that'll make the program inform the user of the current progress of the blast run?
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 ArticleBlast Can'T Find Databases
I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has [BLAST] BLASTDB=/home/bioinformatics/Desktop/blastDBand yet when...
View ArticleBlast_Formatter: How To Choose Which Database To Read From?
Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command:BLAST Database error:...
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
View ArticleHow To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens...
I used PSI-CD-HIT-2D to compare the proteome of pathogen A to pathogen B from the same genus at 30% identity. The matched protein sequences (homologs above 30% identity) are then compared again to...
View ArticleIs Makeblastdb Creat 3 Files Like Formatdb + Blast Error
Hi everyone, I have a big problem!I install blast+ for windows.I run this :makeblastdb.exe -in filename.fasta -dbtype nucl -out filename_BLASTdbapparently it create db coz I have this message:a -dbtype...
View ArticleDifference Between Blastall And Blastn?
What is the difference, other than subtle different in the output format, between "blastall -p blastn" and running NCBI-Blast+ blastn?Are the results supposed to be the same in terms of...
View ArticleNgs Multi-Dataset Analysis
Hello I have some doubts on my analysis of an 454 EST s assembly of data that come from 3 different datasets. Each dataset come from the same organism, but in different conditions (resistance to...
View ArticleBest Blast Hit Without Pain
Hi,This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to...
View ArticleHow To Make A Blast Database With Taxonids From Ncbi Query.
I am seemingly stuck with something that should be very simple and I hope I haven't overlooked something obvious. Question: How can I make a valid Blast-database with Taxids from a NCBI query export?...
View ArticleTutorial: Installing And Running Ncbi Blast
##rest "Installing and Running NCBI BLAST" tutorial imported from the MSU course Analyzing Next Generation Sequencing Data (http://bioinformatics.msu.edu/ngs-summer-course-2011) You should start this...
View ArticleHow To Force Blastp To Display All The Possible Combination Of Alignments?
I want to use blastp to find out all the alignment among two fasta file.Here is my command:blastp -query "A.fasta" -subject "B.fasta" -evalue 1 -outfmt 6 > output.txtI have already set the e-value...
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