Obtaining 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 ArticleStandalone Blast In Bio Python Module
I've been trying to check sequence conservation of target genes with a uploaded database using local blast StandaloneBlast in python. The tutorial is very confusing, can anybody give me link to...
View ArticleLimit The Memory Size Of Blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
View ArticleFinding Protein Homology?
I'm looking for something that's more rigorous than BLAST and less rigorous than a global alignment-esque algorithm. Is there a paper out there that compare methods? What's the most popular method?I'm...
View ArticleMpiblast Vs Blast+
How up-to-date is mpiBlast compared to blast+ from ncbi? I am not sure what the relation ship between mpiblast and blast+ is, is mpiBlast derived from blast+. blast+ seems to be multi-threaded, but I...
View ArticleHow To Parse Psiblast Results Using Biopython And Blast-2.2.24+?
I'm trying to run a PSIBlast program which selects certain sequences out at every round before it does the next iteration. For this I need the Round attribute shown in...
View Articlebioinformatics related problems
hello friendsi have downloaded blast database (rpsd; for conserved domain). but i am unable to us it. so plz can anyone tell me how i can use (untar files of cdd.tar.gz file).thanks:)
View ArticleHow do I generate the correct input files for Blast2GO from CuffLinks2 output?
Hi everyone,Sorry if this is a "no-brainer" type of question, I just started assembling my first transcriptome last week (and am having a really good time learning how to work with all these data!). I...
View ArticleBlastclust Output Problem.
HI,I have installed the blast standalone latest version 2.2.25 with the help of the installation guide http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html. I ran the blast with a 14Mb fasta file...
View ArticleBlast Db Version
Hi all,I'm currently updating my BLAST application from the legacy BLAST to BLAST+. It seems that BLAST+ expects 'version 4' database files. Which my blast DB's apparently are not.Is there a way to use...
View ArticleAlign Multikb Contigs Of A Mammalian Genome Against List Of Mammalian Genome...
I would like to be able to align multi-Kb contigs of a non-assembled mammalian genome against the list of available mammalian genomic assemblies. I would like to do this locally since I have got many...
View ArticleDisagreement When Computing Contig Alignments With Different Tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
View ArticleFind All Similar Sequences In Genbank
Hi, I would like to get a feel for how many sequences related to my virus of interest are available on GenBank. I am thinking about using a recursive BLAST approach. Start with one genome, BLASTn, and...
View ArticleIs There Any Api Of Blast And Uniprot To Align Protein?
Given a set of protein's gi/UniProt identifiers. I want to find the e-value/identity between each of the pairs. I decided to do it by program but I cant find any apis of Blast and Uniprot. Any ideas?
View ArticleMakeblastdb Help
Hi,I feel I'm being really dumb here, so please excuse me! I have a file of fasta sequences which I want to make into a blast databse for standalone blast.I haev the fasta file saved in the bin folder...
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 ArticleRetrieving Protein Structures
I want to make structural analysis of lysosomal proteins found in mammals. To make start, I would like to retrieve as many structures as possible from the biological database (PDB). These structures...
View ArticleParsing Blast Results For Different Genus
Dear All,I have obtained several .gb BLAST results that I want to split in different .gb or .fasta files accordingly to genus.I searched for different ways to do it in the web, but didn't find a way to...
View ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
View ArticleObtaining the top matches from blast
Hi,I have downloaded the current version of the stand-alone-blast (ncbi-blast-2.2.29+) and I am trying to use blast (blastn) to find similarity of of a group of nucleotide sequences that I have....
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