Blastclust Ignores The Multithreading Argument (-A)
I'm trying to run:blastclust -a 48 -p T -d ./uniprot/2011_04/all.fasta -v progressI have 48 cores on the server thus -a 48 argument, but only 100% CPU (1 core) is used.I have Blast2 version 2.2.21...
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 ArticleUsage Of Format Specifiers For Blastx In Ncbi Standalone Blast
Hi to all I am doing blastx with ncbi standalone blast for large number of sequences. I am getting the output in outfmt -7 (tabular with comment lines). There are 'keywords' like frames/qframe/sframe...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
View ArticleHow Long Should It Take To Make A Blast Database?
HiI'm trying to install a local copy of polyphen and one of the stages is to make a blastdb from uniref100.I ran this command last night and its still going nearly 12 hours later. I don't know if this...
View ArticleHow To Run Genome Wide Local Blast
Hi Everyone, I have been given a task to compare one gene sequence among 50 strain of E.coli. For this study i have 50 genome scaffold file and one gene sequence file. Now my work will be compare the...
View Articlegetting error in runing tblastn
Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue...
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 ArticleAlignment Of Thousands Of Short Rnas To Local Database
I have a fasta file of about 200,000 RNA sequences and a server holding a local copy of Rfam. For each sequence I want to know the type of RNA it is most related to and ultimately retrieve statistics...
View ArticleAverage nucleotide identity
Hi,I'm using ANI to determine if two bacteria species are related or not. What is the threshold for saying two sequences come from different species ?
View ArticleHow to create a Blast database of viruses ?
Hi all,For a metagenomic project a want to make a blast database of viruses. I dont want to blast my reads on the entire nt database. But I dont know how to make it. Downloading the result of a query...
View ArticleBlast+ Stand Alone Version For Sequence Alignment
HiOn the on line version of Blastp (link text) there is a sequence alignment section (and it produces E-values for the alignment).and now I want to use the standalone version to perform alignment(My...
View ArticleWays To Quantify Proteome Analysis Via Blast
I'm working on software to allow users to blast an entire proteome against a manually curated database in order to attempt to quantify the composition of that organisms proteins against our database....
View ArticleWhat Makes A Valid Gi List?
Hello all, I cannot figure out what makes a "correct" GI list!Atm I have a list that I produced this using the query below and a awk line to just retrieve the second column values blastn -word_size 11...
View ArticleWhat'S The Easiest Way To Blast 5000 Sequences Against An Exon Fragment?
I have 5000 EST sequences that I downloaded from Genbank. I have a 500 bp exon fragment that I'd like to BLAST against this lot of sequences to see if my exon is present or not. What's the easiest way...
View ArticleWhy The Default Expect Threshold In Pblast Is 10?
Hi;In pBlast the Expect Value is used to limit the number of scores and alignments for reporting matches against the database sequences. The default value is assigned 10 (NCBI Document: link text)...
View ArticleHow Set A Pssm (Position Specific Scoring Matrix) When Querying With Blast+?
help me out if anyone knows the answer for my question, How to search a nucleotide database using PSSM ( i developed the PSSM using set of protein sequences from query set) Do provide me the command in...
View ArticleImport Xml Blastx Results In Geneious
Hi,I have the xml results file of my local blastx and I would like to import the annotations directly on my sequence in geneious. Do you know if there is a way ?Thanks,Aurelien
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
View ArticleIs Blastall Only Using Blast, Not Blast+?
Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.
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