Comparing Bowtie H_Sapiens_Asm Blastn -Task Blastn-Short -Db Human_Genomic
I am thinking the current supplied (pre-formatted) blastn humangenomic database from NCBI contains many many duplications of the same sequences. Is this correct? I think I only need the current...
View ArticleGetting Taxonomy Lineage From Ncbi Gi Or Accession Number
Hey GuysI have a specific question about getting a taxonomic lineage, given a NCBI accession or GI number. I have in the past used the module from CPAN (below) but I belv it only works for GI's and not...
View ArticleAny Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View ArticleNcbi Non-Redundant Dataset (Nr) In Protein-Blast To Look For Homologs?
Hi all,this must be very basic, but still. I have a protein sequence for which I want to find homologs. I go to BLAST and do, for simplicity here, a regular BLASTp.I know that blasting against...
View ArticleSetting E-Value In Blast
Hi,Again I realize that its an easy question :). Could anyone tell me how to set e-value to 0.005 in Blastp?
View ArticleExtract 100 Downstream Sequence Of The Aligned Sequence Of Blast.
Hi all,I need to get 100 downstream of the nucleotide sequence from aligned results of the web blast query.Is there any way to get the required sequence from NCBI?
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 ArticleBlast2Go Save While Working
Hi I am running blast2go for a huge set of sequences. I would like to save the blast results from time to time (in case there is some problem with the computer, not to begin everything from the...
View ArticleGene ID conversion and Pathway analysis after mosquito blast
Hi all I have got my blast result from mosquito Contigs Fasta format. Sth like query_name query_length accession_number 1059N_ae_contig_1 676 XM_001650645 1059N_ae_contig_5 563 XM_001650988...
View ArticleProblem Parsing Xml In Biopython
Hi mates, I m new in python and I m trying to parse a result from local Blast...here the code.from Bio.Blast.Applications import NcbiblastpCommandline from Bio.Blast import NCBIStandalone from...
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 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 ArticleStandalone blast results wrong
Hi,I downloaded the NR database from NCBI about 2 months ago. The past few times I have run a blast search on some contigs, the results have been wrong on many of the query sequences. I checked this by...
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 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 ArticleDownload Ensembl Blastn Result
Hi,How can I download blast results from ensembl. I blast 10 sequences against all ensembl species. Now I have the result page and I want to download all hits to compare them.Is it possible ?Here's the...
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 Articlerecruitment plot - blast output
Hello Guys,Does anyone have a tutorial for generating recruitment plot from a file output blast? thanks!
View Article/Home/Abc/Ncbi-Blast-2.2.25+/Bin/Blastn: No Such File Or....
Hello, I want to set a local blast in my system..but it showing some error while i am working. I have set Environment var path /home/abc/ncbi-blast-2.2.25+/bin in .bashrc file. i also have set the...
View ArticleHow to remove redundant and poor quality ESTs
Hi community, i have a question that, How to remove redundant and poor quality ESTs from whole data set through online .......?
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