NCBI blast PHP API choice
Hello.I want to program a web application, based on PHP language. One of its features, will be the ability to send data and receive results to/from ncbi's server and then analyze them with other...
View ArticleHow to perform BLAST search containing a large number of query sequences ?
I need to BLAST a large number of query sequences in one go. How might I go about this ? I have a .rtf file containing a large number of query sequences ... in this...
View ArticleDiamond database creation
Hello,I just installed the Diamond Protein Alignment Algorithm (http://ab.inf.uni-tuebingen.de/software/diamond/) yesterday and the first step before the alignment is to set up a database. The input...
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 ArticleBl2Seq In Blast+
I have recently installed blast 2.2.24+ and I was looking for the bl2seq tool, but I didnt find it. After some research I found that bl2seq is only found in the legacy blast package. So my question is...
View ArticleAre The Query Strand And Hit Strand From Blastx The Same Strand?
I'm writing code to parse the XML output from a BLASTX search on NCBI's servers, and from this grab from NCBI the nucleotide sequence whose translated protein was found to be a hit by BLASTX . This is...
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 ArticleAny Way To Ncbi Blast Multiple Protein Sequences?
Is there any tools or any direction anyone can point me in towards Blasting multiple amino acid sequences on http://blast.ncbi.nlm.nih.gov/Blast.cgi ?I could potentially write a script to do this and...
View ArticleHow To Find The Locations Of A Short Specific Sequence In A Genome With 1 Or...
We have a 23 nucleotide CRISPR target sequence of which I would like to find out if it also present in other locations in the genome. The sequences directs a CRISPR RNA construct to introduce a indel...
View ArticleBlast Can'T Find Databases
I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has [BLAST] BLASTDB=/home/bioinformatics/Desktop/blastDBand yet when...
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 ArticleCorrect Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Hi all,I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking...
View ArticleExtracting Query Sequence From Blast Xml Output Using Ncbixml Parser
I want to Blast my data base of sequence (Aminoacid) with a data base. And get sequences which have a given score and e value less than 0.5 . So I ran blast with e-value 0.5 and now i want to isolate...
View ArticleHow To Extract Max Score Blast Hit Among A Data Set?
Hi everyone, I performed a local blastp with a query protein vs 5 genome (ORF data ). Now i want to extract all the top 5 sequence automatically and make a final top hit file through awk/perl/shell....
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.
View ArticleOrf Finder Vs Blastx
This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast...
View ArticleHow To Scale A Pssm For Ncbi Blast
Hi again,I'm trying to do a local NCBI BLAST search using the PSSM of a conserved CDD domain (.smp file in the database, cave LARGE file).My database is containing nucleotide sequences and the PSSM is...
View ArticleWhy am I getting the BLAST option error: file does not match input format type
COMMAND USED: makeblastdb -in sorted_alu_seq.fasta -dbtype 'nucl' -out aluBLAST option error: sorted_alu_seq.fasta does not match input format type, default input type is...
View ArticleRetrieving Complete Cds From Ncbi
Hi,I was trying to retrieve complete cds sequences from NCBI for a certain protein of interest, say acetyl coa transferase. I did an advanced search as below:((("acetyl coa acetyl transferase"[Protein...
View ArticleIs there any free ultra-fast resource for doing blast?
Dear all,As far as we all know, doing blast in the NGS filed is really time-consuming and impossible in the routine way. Could anybody please let me know is there a free ultra-fast resource to be able...
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