What'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 ArticleHow To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.But how to create it? There is a makemat...
View ArticleOpening A Fasta File In Windows
Hi all,I am a beginner with Blast+.I am using Windows.My aim as of now is to download the nr protein sequence in Fasta format and then format it using makeblastdb.then extract the first 1000 characters...
View ArticleFormatdb From A Batch Of Fasta Sequences
Hi I have a batch of fasta files, each one is a file of ESTs from a different plant. I want to create a database for all the plants, how can I use formatdb (or another way) to create one database which...
View ArticleLocal Fasta Query Using List Of Gi Accessions
Is there a quick and easy way to query a Fasta (.faa) file using a list of GI accessions and generate a report? I already have the ncbi-blast program installed and amended the $PATH environment.
View ArticleWhat Exactly Does Formatdb Do?
As far as I know, the blast searches for homology in the way that indexing query(word list), scan database(automaton), extension and so on. Then why should we pre-process the database with formatdb.I...
View ArticleBlast Result Matching Both Of Two Query Sequences?
If two short sequences (A and B) come from the same gene, but I don't know the name of the gene or the organism, can I perform a BLAST (or similar) search to find the gene which has best similarity...
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
View ArticleNcbi Blast Two Parameters'S Question
Hello, I don't know NCBI BLAST two parameters, here they are: -num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Default = `500' -num_alignments...
View ArticleUse Megan To Parse Sam File
Dear all, I got a question about using MEGAN4 to parsing SAM file. What I want to do is to get taxonomic and functional annotaion of my raw reads against nr database . As the raw reads is too big (11...
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
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 ArticleIs there a succinct method of isolating sequences phylogenetically similar to...
This is a bit outside of my wheelhouse so I apologize if some terminology is incorrect.I have a number of reference RBCL gene sequences for a taxonomic family, and I want to extract sequences from a...
View ArticleCustomize Link To Ncbi Blast Search
I want to insert a link to NCBI Blast search into web page with given GI and coordinates. Link like this:<a...
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 ArticleAssigning subject to query based on coverage from blast output file
Dear all, I have blast result in tabulated format. Each of the query hits multiple subject sequences. From all of those hits, I want to assign that subject sequence which covers the query sequence the...
View ArticleHow To Differentiate Databases When Blasting From The Command Line?
Hello, I'm creating a python script to take each ORF from a genome and blasting it against 3 other genomes in order to retrieve common and unique ORFs for the query genome. I am using Bio.NCBIXML to...
View ArticleHow To Get The Result Which Mismatch 1 To The Query Sequence By...
the program is blastn -task blastn-short -query rfam_trimed_short_uniq.fa -db /root/bio-analysis-soft/database/gss-est-db/tage -ungapped -penalty -1 -reward 1 -outfmt 6 -out 2 -num_threads 12I get an...
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...
View ArticleAligned Ranges In Blast
I have several sequences which I'm blasting against the nt database, and I wanted to know how to retrieve for each hit the intervals matched. As far as I'm aware, the standard output only gives this...
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