Blast 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 Generate Blast Database
Hello I downloaded some database in gemnomes/Bacteria ( ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Acetobacterium_woodii_DSM_1030_uid88073/ ) I want to use blast program. I have some problem. How can...
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 ArticleMakeblastdb Can'T Find My Fasta Files
I'm trying to make a nucleotide database for my sequences. After opening C:Program Files\NCBI\blast-2.2.28+> in the command line, I typed in makeblastdb -in test_gene.fsa -parse_seqids -dbtype...
View ArticleHow Could I Run A Huge Number Of Blast Calls Faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
View ArticleEmbedding Blast Tool In A Website
I'm planning to include BLAST search tool in a website to search against my own databases where user can choose one of the two databases with all the optional blast parameters (e.g. E value cutoff,...
View ArticleAny Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View ArticleAny Way To Ncbi Blast Multiple Protein Sequences?
Is there any tools or any direction anyone can point me in towards Blasting multiple amino acid sequences on http://blast.ncbi.nlm.nih.gov/Blast.cgi ?I could potentially write a script to do this and...
View ArticleNcbi-Blast+ Version 2.2.23 'Make' Error
I'm getting errors when I run 'make' for rmblast-1.2-ncbi-blast-2.2.23+-src. This is the version of RMBlast modified for use with RepeatMasker from their site. I had no problem installing it in Ubuntu...
View ArticleBlast Xml Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
View ArticleBlast Contigs To A Reference Sequence And Obtain An E-Value
Well, I'm a newbie of blast, so...hope I'm not asking a stupid question....I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align...
View ArticleHelp In Configuring A Local Blast Server.
Hi all.I am attempting to configure a local BLAST server on a Windows XP machine. I found the following series of explanations helpful but incomplete:http://www.ncbi.nlm.nih.gov/books/NBK52637/Relevant...
View ArticleBest strategy to get GO terms for a proteome?
Hi,I would like to know the best strategy to get the highest amount of GO terms for the bacterial proteome I'm working. Since it's a non-model organism, I will build the GO database from scratch.I...
View ArticleConverting Blast Results In Fasta Format
Hi, I "blast" my protein sequence against the NCBI database and I wish to save the returned results in FASTA format. Is there a way to convert the sequences all into FASTA format and save them or do I...
View ArticleAlternative To Local Blastplus To Blast 10000'S Sequences On Nr, Swissprot...
Hi,Here is a case scenario that happens quite often to me: I need to blast from 1,000 to 20,000 sequences in order to find the proteins these sequences code for. These sequences come from fish cDNA...
View ArticleHow Reproducible Are The Results Programs Compiled With Blast Libs Vs Calling...
Is there a risk that using the blast libs to do blast work could result in reproducibility issues if someone were to spot check the results with the NCBI executable? I am working on a program to do...
View ArticleShowing Queries With No Hit In Tabbed Blast Output?
Hi, I was wondering if anyone could tell me if there's a way to get the tabbed BLAST output to show if there's not hit. I don't mind using either blastall or blast+.The reason I ask is that I'm trying...
View ArticleForum: Looking For Help To Understand Bioinformatics Papers On Blast, Yasara...
Hello, I'm a student and i've got to make a paper about bioinformatics i've been working on it for a while and i'm almost done. I only have to write about BLAST, YASARA and the huntington disease...
View ArticleParsing Blast Output Biopython Error
Hi, I have the following code def runBLAST(self): print "Running BLAST .........." cmd=subprocess.Popen("blastp -db nr -query repeat.txt -out out.faa -evalue 0.001 -gapopen 11 -gapextend 1 -matrix...
View ArticleTools For Validating Blast Result?
Hi Friends,After doing blast for my nucleotide sequence i have found out the homologous sequence based on the identity, sequence coverage and e value. Kindly tell me which tool will be best to find out...
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