Compute Blastx E-Value
Does anyone know how blastx e-values are computed? Is it the same as blastp, except the query sequence is divided by 3? I've tried using E = (m/3)n2^(-S), but I get slightly different results than from...
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 ArticleHow Can I Batch Blast Sequences To Identify Them?
I have a list of 189 Accession numbers for 16s rRNA, how can I batch BLAST these to find which species they are closest too? I tried this server: http://greengene.uml.edu/programs/NCBI_Blast.html but...
View ArticleScientific Names In Blast Output And Databases
Hi, I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option -outfmt which can take sscinames(seems new in version Blast+ 2.2.28), but even...
View ArticleRetrieving Results Using Blast Soap Api
Hi ; I have a problem with using Blast SOAP API. Previously, I used the downloadable version of blast in which I balstp against PDB using the following command line:"blasp.exe -query input.txt -db...
View ArticleCustom Matrices With Ncbi Blast
Does anyone have an idea on how to make NCBI BLAST work with custom Matrices? i.e. ones that are not provided by the BLOSUM series that come as a default with NCBI BLAST.
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 ArticleGenerating Protein Consensus Sequence For Blast Input
I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.how should I go about it?
View ArticleProblem In Making Blast Database (Makeblastdb)
Hello, I am confused by BLAST. This is the problem: I have made a fasta file as following>1|DNA (cytosine-5)-methyltransferase 3A MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPV...
View ArticleAssemble Reads According To Blast Result
Dear all, I performed blast using ~200 gene sequences from reference organism against a draft genome dataset from related species ( containing 12million short reads(sr), each of which is 88bp). The...
View ArticleBlast+ Error Code=12
Something really bizarre is going on. I ran 6 tblastn jobs independently using the following command line entry: tblastn -query blastqueries14920.fasta -out blastqueries14920.fasta.out -db...
View ArticleMissing BLAST hits - max_hsps and max_target_seqs?
Hi, I have a single file that contains 10,000 query sequences, each 300bp long. The subject is a single chromosome that I have imported into a nucleotide database ("makeblastdb -dbtype nucl"). Due to...
View ArticleBLAST: How much of the query is aligned?
At first, I thought this question would answered by the "qcovs" field, but a glance at the results proved that that isn't the case. To begin with, each qcovs value relates not to the original query,...
View ArticleBatch Blast Two Sequences And Output Sequence Alignment
Dear all,I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.FILE1>gene1_species1...
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 ArticleMerging Blastx Hits From Overlapping Bacterial Genome Segments
I blastx-ed 1Mbp bacterial genome fragment against NCBI nr database. I have split it into 2000bp fragments with 500bp overlap into a one multiple fasta file (splitter from EMBOSS) splitter -sequence...
View ArticleAn Error By Using Ncbi-Blast-2.2.25+ (On Windows)
Hi all I downloaded blast+ software package (for windows), and installed like theBookshelf; to run it i used this "ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out...
View ArticlePipeline Or Tool For Going From Assembled Genome Fasta & Gff Files Directly...
I'm hoping this doesn't come off as a lazy question, but I am wondering if anyone is aware of a tool or pipeline out there that directly takes reference genome (supercontigs, contigs, scaffold, what...
View ArticleScientific Notation In Blast
Hi there,I've to choose some sequences from blast result which are under 10^-5 Results are in scientific notation. How can I convert scientific notation to double? Which is the double for 2e-104 ?Thank...
View ArticleError Using Makeblastdb
Hi there,I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta...
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