BLAST: Querying a single sequence without input file in C
This is with reference to the query posted in https://www.biostars.org/p/17265/. If I try to run the following using command line it runs perfectly fine: blastn -query <(echo -e...
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 ArticleAffine gap penalty in Megablast
Dear all,I have a question. In megablast I don't understand why the existence and extension gap penalties in affine model are in that way. I thought the existence gap score must be always larger than...
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 ArticleDifference Between Blastall And Blastn?
What is the difference, other than subtle different in the output format, between "blastall -p blastn" and running NCBI-Blast+ blastn?Are the results supposed to be the same in terms of...
View ArticleWebtool For Fetching Pmids From Blast?
Hi, I was wondering if there is a web service that extracts all of the PMIDs that are in the results for a BLAST search? Example: I input the sequence for enchanced FLP and get a list of all the PMIDs...
View ArticleWhere can I download the blast version that includes formatdb ?
I am trying to use a pipeline that uses formatdb command of old BLAST. This option is been replaced by makeblastdb in newer versions of blast+ . I could not find archive for blast to download the old...
View ArticleProtein Sequence Homology Score, Align Or Blast
Hi,I want to get homology scores for every pair of human proteins acoording to their sequence amino acid constitution. should I blast these pairs(blast2seq) or align these pairs(localAlignment)?
View ArticleBiopython Local Blast Not Producing File
Hello, I am a Computer Science & Molecular Biology Student at MIT. I am currently working on my research project in the Research Laboratory of Electronics and I am trying to solve a problem while...
View ArticleHow To Show More Blast Results Using Biopython?
Hi,I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't...
View ArticleConvert Blast Output Into Blast-Xml
Hey!Problem: I need to convert a standard Blast report into the blastxml format.Background: For speed reasons, I am using UBlast (Usearch) instead of NCBI-Blast. UBlast outputs either tab-delimited...
View Articlencbi-blast warning: Selenocysteine (U) at position ** replaced by X
Hi all, I just want to know what does this warning message means.There's a way to suppress blast+ warings? The old blast has a flag -warnings as parameter, but the blast+ doesn't.
View ArticleForum: Looking For Help To Understand Bioinformatics Papers On Blast, Yasara...
Hello, I'm a student and i've got to make a paper about bioinformatics i've been working on it for a while and i'm almost done. I only have to write about BLAST, YASARA and the huntington disease...
View ArticleBlast2 Vs Ncbi-Blast+
In my debian testing system I have two blast packages:ncbi-blast+ 2.2.25-7 with homepagehttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/and blast2 1:2.2.25.20110713-3 with homepage...
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 ArticleIs there a way to run ncbi blastx so that its result will contain GO (gene...
I've already tried BLAST2GO and it is either running too slow or unable to connect to its database.So, I was just wondering if there is a way to run blastx in a particular way with some parameter so to...
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 ArticleHow To Automate Primer Blast With Perl?
Hey all!does any one have a PERL script for automating the PRIMER BLAST tool.... i.e. i want a script which will submit my fasta file and parameters to Primer BLAST and retrieve the output. I'm stuck...
View ArticleNcbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
View ArticleForum: Question: HOW TO STORE BLAST RESULT INTO DATABASES using Python?
I am comparing sequences with databases using NCBI command line blastall. Now, I wanted to store the results into Databases like SQL or Access or Whatever using Python Script ??????Somebody will tell...
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