Applying A Pssm To Psi-Blast
I'm able to generate a PSSM and a sequence from combinatorial experimental data. I want to BLAST the results to find proteins displaying these motifs. However, I have information about each position's...
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 ArticleOnline blast and standalone blast return different hits?
Lately I have issues with blast. Anyway what I want to do could have different and easier process so I welcome any help. I have a list of cow protein sequences(many, about 200 sequences) and I want to...
View ArticleHow to perform phylogeny analyses
i want to do project on phylogenetics on hiv subtype-1.but how i start the project on this ,what tools are apply on this.
View ArticleCommand blast excluding species
Hello,When using NCBI's interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?I need to exclude one species from my search. I see this can somehow be done...
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Configuring Path To Point To The Bin Directory Inside The Ncbi Folder After...
I can't seem to get Terminal to accept the syntax described on NCBI's help page regarding configuration of the standalone BLAST installation. Here's my syntax and the error messages:
View ArticleBlastn Runtime 606 Queries
When I run blastn -numthreads 6 -task blastn-short -db humangenomic on one 36 bp query it typically takes less than a minute and occupies up to about 5GB. When I gave it a file (using -query) of 606...
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 ArticleDefault Frameshift Penalty For Blastx
I do not set the frameshift penalty costs and output everything in BLAST XML format. Then I go through this file and usually the beginning contains parameters of the scoring scheme etc. But it does not...
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 ArticleHow To Use Blast To Find Exact Matches Of Short Sequences?
Hi, I am using tblastn (under blast 2.2.25+) for exact peptide mapping (no gaps). I want to map few peptides (about 6 to 50 AAs in length) to genome. However, as I test a known peptide of 6 AAs,tblastn...
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 ArticleQuerying blast and getting raw hit fasta sequence
I have downloaded refseq_rna database and I want to query this database on my standalone blast with tblastn. I have many queries and what I want to achieve is to not only get blast alignments but also...
View ArticleForum: Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver
Executive Summary: SequenceServer lets you rapidly set up a custom BLAST+ server with an intuitive user interface for use locally or over the web.Why we created it: We were frustrated with:too many...
View ArticleParse Blast Output ..
i want to parse this blast output but compilers giving NULLPOINTEREXCEPTION .. input file and source code of java program is given below ... plz help me out..Exception in thread "main"...
View ArticleConverting ANY blast output file to an alignment fasta file.
Hey there guys. We use the Blast Command Line toolkit to Blast populations against each other. We created a database of transcriptomes of one population and then used the blast command line kit to...
View ArticleMasking repetitive sequences ...can I then map using BWA?
Hi thereIn need of help please!I'm masking the repetitive regions in my wheat sequencing data using RepeatMasker. This generates a .masked file. Next I want to map or compare this masked file to other...
View ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View ArticleMake A Dotplot From Blast Alignment
Hi all,I am a complete beginner with blast. I used the NCBI online service for aligning two sequences, and got a nice dotplot representation. Now I am running blast on my pc, and I would like to obtain...
View ArticleHow to get BLASTP output using URL only in XML format?
This is how I am doing it right nowI go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthomePaste query sequenceSelect pdb as databaseSelect...
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