Customize 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 ArticleBest way to grab all NCBI protein sequences for a specific taxonomic query?
I would like to retrieve all of the NCBI protein sequences that belong to a specific taxonomic query, or children of that query. For example, I want to get every protein sequence belonging to the...
View ArticleDisagreement when computing contig alignments with different tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
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 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 Articlesequence blast against RFam database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
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 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 ArticleProviding Private BLAST Access to Different Users
Hello all,I have a number of collaborators working on different RNA-seq/genome projects. Each group has its own genes assembled from RNA-seq, on which they like to run BLAST and other analysis. Also,...
View ArticleBlast to Cytoscape
Hi Guys, I am trying to view the results of an all vs all blastp of some sequences with cytoscape. I've been using the Blast2SimilarityGraph app to read in my data (blast -m 8 + fasta file) and then a...
View Articleformat uniref90.xml to database for BLAST
we want to get a formated database for BLAST from Uniref90. we referred an article which used an early release Uniref90, say version 10.0 ftp.uniprot.org only provide the XML format of this version....
View ArticleBlast contigs to a reference sequence and obtain an E-value
Well, I'm a newbie of blast, so...hope I'm not asking a stupid question....I've already have a set of contigs which is done by de novo assembler. Format of these contigs is fasta. Now I want to align...
View ArticleHow to downlad blastall executable
Hi,It seems that the old version of blast (blastall) can make use of multithread processing and speed up things whereas new blast+ versions get stuck to using single thread even when you set the...
View ArticleStrategies to blast against fastq files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View ArticleHow to cluster sequences based on BLAST results?
I want to cluster a set of DNA sequences into families based on BLAST results. Is there any idea what software I can use to do it? Thanks!
View Articlehow to build the correct BLAST url for the REST interface
Hi All,I am having difficulties constructing a BLAST query via the REST interface. In particular I would like to have a defline via QUERY_BELIEVE_DEFLINE and actually submit two sequences. The URL I...
View ArticleWeb BLAST Apache configuration (Error 403)
Hi,I'm trying to run Web Blast 2.2.28+ locally trough Easy PHP Dev Server 13.1 (Apache 2.2, Windows 7), but when I click on search it shows ERROR 403 when I open it within my site or the following...
View ArticleSequenceServer: 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 ArticlePython program accepting FASTA and BLAST, outputting in XML then returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleGiven sequences, how to compute a low complexity score for each sequence?
Is there a way or a program/module that I can use to compute the complexity score for the given sequences? I want to rank sequences by their complexity.
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