Blast_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 ArticleHow To Blast Consensus Sequences With Bacterial Genome?
Dear all,Subject- To find number of hits available for the particular consensus sequence in bacterial genomeI am having this consensus...
View ArticleBlast Execution Problem
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
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 ArticleHow To Get Blast+ (Stand Alone Blast) Output To Contain Only The First Hit...
Greetings! I'm using BLAST+ v. 2.2.26, and would like to customize the output to include only the FIRST hit for each separate record in the data base. The region I am using as the query is a domain...
View ArticleTblastx Exception Error
Hi,I am having some problems running tblastx locally on my HPC. I built my own database and I am trying to run tblastx on a small data set (to then move into larger analyses) but I am getting an error...
View ArticleWindows Cmd Not Responding With Python Blastall 2.2.17
I'm using the standalone BLAST 2.2.17 with python. However, I'm having a problem with the cmd. When running the script the cmd stops responding at the 15th blast record. It doesn't matter if I change...
View ArticleBlast Illumina Probe Sequence To Get Their Genomic Coordination
Hi all, The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am...
View ArticleStrategies To Blast Against Fastq Files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View Articleblast against genomes in biopython
from Bio import Entrez, SeqIO from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast("blastn","nr",...
View ArticleAre There Local Aligner Like Blast Working On Unicode Characters?
I want to use a blast-like local aligner to find common substring between common human readible texts. e.g. social media data. A normal plagiarism finder won't do because the intention is to align GB...
View Article[Fastacmd] How To Retrieve Sequence From Blast Db
Let's say I have multifasta with protein sequences having internal IDs (integer)>1234 MGKL...*I build blast db using:formatdb -i infile.fa -pF -n someDBBut then, I'm unable to retrieve sequence from...
View ArticleRepetitive element coverage of consensus
I have a consensus sequence for a class of repetitive elements (from repbase) and I want to find out the depth coverage of the real genomic instances (taken from ucsc rmask table) against this...
View ArticleWhat Substitution Matrices Are Available For Blast?
I'm having trouble locating documentation on what substitution matrices are supported by command-line BLAST+ tools. Do they have a specific set of matrices built in? Are they hidden in a directory...
View ArticleBlast2Go Doesn'T Work With My Fasta File
Hi all, i downloaded human unigene fasta file from Here (Hs.seq.uniq.gz with .uniqe format), and change it to .fasta by notepad. when i submitted the file to blast2go it doesn't work and give me an...
View ArticleHow To Blast Multiple Contigs To The Reference Database?
i have multiple contigs in fasta format after assembling the reads. i also have 33 reference genome sequences. i want to blast the query sample sequence to my reference sequences as well as the plasmID...
View Articlehow to find different gene loci between two strains
I already have two complete genome,I want compare them to find different gene loci and related proteins.how can I do that?I read some papers about this,one said use blastp and then COGs,but I don`t...
View ArticleConvert Blast Output Into Blast-Xml
Hey!Problem: I need to convert a standard Blast report into the blastxml format.Background: For speed reasons, I am using UBlast (Usearch) instead of NCBI-Blast. UBlast outputs either tab-delimited...
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:...
View ArticleError '"use" not allowed' when running a bioperl script
Hello all i would like to blast multiple sequence individually one after another and output i need in excel sheet, i tried like this: use Bio::Tools::Run::StandAloneBlastPlus;...
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