Blast Settings For Short Sequences
I'm searching for short sequences in nt. By short, I mean 10-20 bases. When I run blastn, I get no results, regardless of my -evalue settings. Here's the test sequence:>ponzr CGCGGTAAAACACATTTG And...
View ArticleDefault Ncbi Blast+ V. 2.2.25 Parameters
Hi:I'd like to compare my own BLAST tool with NCBI blast+ tool but couldn't find the default parameter of this version. I'd like to know the scoring scheme for match, mismatch, opening gap and extended...
View ArticleI Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found...
This is the errorBLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/aj3/Desktop/h/database::]what should I do? do I have to use any other commands...
View ArticleError When Using Makeblastdb On A Large File
Dear All,I have created a stand alone blast on my system, to work with NGS data and it is working fine. However, I have got a sequence file which is about 2400MB, which is two large to create a local...
View ArticleFormat Uniref90.Xml To Database For Blast
we want to get a formated database for BLAST from Uniref90. we referred an article which used an early release Uniref90, say version 10.0 ftp.uniprot.org only provide the XML format of this version....
View ArticleFrom Blast To Ucsc Genome Browser: Valid Loci
Hello,BLAST, sometimes, does not propose direct links to Genbank pages as reports, and this leads to unaccepted entries in the UCSC Genome Browser's search term box. How could I avoid those results? Is...
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
View ArticleBlast Motif With Regular Expression ?
Hi there =) Today I was asked if there is a possibility to BLAST (blastp) for a specific amino acid MOTIF spanning seven amino acids. However this MOTIF is 'dynamic' at 3 points: position 2 in the...
View ArticleBlastx With Xml Format
Hi all, I'm currently using standard alone blast, the version is ncbi-blast-2.2.25+. I tried to made xml format blast result for my downstream analysis, but I had some problems in generating it. The...
View ArticleBioPython : comparing same sequence with two different databases
I compared query sequence with two different genomes( Genome1 and Genome 2) individually using Standalone BLAST and saved in two different files. Now, I wanted to store these information in following...
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 ArticleExact Matching With Bowtie, Blat And Blast+
I am running bowtie with the following parameters, to look for up to, say, 10 exact matches of a 36-base nucleotide string to a GRCh37/hg19 index, _e.g._: $ bowtie -S hg19 -v 0 -k 10 -f sequence.fa...
View ArticleMEGAN5 - input blast -m8 option problem
Hi, I am trying to run MEGAN5 using a blast table generated by an associated researcher. I know that MEGAN is able to interpret blast files fomatted by the m8 option. I have tried to load the tables...
View ArticleIs A Gap At The Same Position In Query And Template Possible?
Hi:I was wondering if a gap at the same position in query and template sequence is possible. Is that from a biological point of view possible or not?As example:ACTCC--CT ACTCCC--GThanks Beeth
View ArticleWhat Is The Algorithm Behind The Sequence Comparison In Uniprot Or In Any...
Hi, This is Shrujan, i wnat to know the algorithm behind the Sequence comparison in Uniprot or in any other database, which does BLAST. I need your valuable suggestions and guidance.Thanks &...
View ArticleShow Progress (Bar?) For Blast+ Query
Hello everyone,It is possible to visualize the progress of a local blast+ (verbose mode or something [maybe python ou perl])?Thanks in advance!
View ArticleMost Sensitive Method To Search 100-1000Bp Sequences To Genome At Human-Mouse...
Following up on this question: http://biostar.stackexchange.com/questions/8010/searching-200-400bp-matches-against-mammalian-genome-human-mouse-distance I would like to know what is the most sensitive...
View ArticleMakeblast Db Problem
I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txtI put...
View ArticlePython/Perl Script For Defining Minimum Coverage Of Blast Match
Hi - does anyone know of a script that allows for a blast result to be filtered by the minimum total coverage of the query/subject that the alignment/s represent?I'm imagining a script that calculates...
View ArticleMining Ortholog Cliques
Does anyone have experience working with mining cliques from ortholog data? I have orthologs generated by best reciprocal blast from 22 species. It is 21 Ensembl species with one species we are...
View Article