Are There Local Aligner Like Blast Working On Unicode Characters?
I want to use a blast-like local aligner to find common substring between common human readible texts. e.g. social media data. A normal plagiarism finder won't do because the intention is to align GB...
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 ArticleNcbi Wgs/Nt/Env-Nt Databases
I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was...
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 ArticleAligned Ranges In Blast
I have several sequences which I'm blasting against the nt database, and I wanted to know how to retrieve for each hit the intervals matched. As far as I'm aware, the standard output only gives this...
View ArticleWhy When I Use Blastdbcmd With The Fasta Database It Doesn'T Recognize The...
nr database is presented in two version. One is the FASTA and there is another one.
View ArticleHow To Generate Blast Database
Hello I downloaded some database in gemnomes/Bacteria ( ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Acetobacterium_woodii_DSM_1030_uid88073/ ) I want to use blast program. I have some problem. How can...
View ArticleDownloading Fasta Files
i need to download about 40 complete genomes from ncbi and still filter out sequences between specified bps(like btn 1000bp to 3000bp) from the genomes separately. i need help on how to do that. i...
View ArticleHow To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
I saw that tblastn is capable of doing that kind of search, but I want my position-specific scoring matrix (pssm) to be built from nucleotide, not protein, sequences.Has anyone done something similar...
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 ArticleMake A Custom Blast Library Using The Output Of Another Blast Result
Hi Biostar,I am working on a microbial gene annotation project and I am interested in taking a large number of sequences (say 20,000) and blasting them against the NR database. However, even with a...
View ArticleOld Blastall Vs New Blastall
I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new computer. I wanted to test the new version of blastall with a lamprey genome database and sequence that works...
View ArticleComparing Genome Derived And Cdna Derived Protein Sequences
I've two sets of protein sequences for a particular organism for which the genome sequence is available to us.One of the protein sets is derived from comparing the genome with all the proteins of a...
View ArticleHow To Examine Whether Homology Search Method Used(Blast/Hmmer) Is Feasible...
Hallo...how to one examine whether homology method used is feasible for identification of a particular gene family e.g HSP. Suppose i have identified 550 sequences suspected to be a particular gene...
View ArticleHow Reproducible Are The Results Programs Compiled With Blast Libs Vs Calling...
Is there a risk that using the blast libs to do blast work could result in reproducibility issues if someone were to spot check the results with the NCBI executable? I am working on a program to do...
View ArticleCan I Have Blast Return One Hit Per Species
Hello all, I've been long troubled with redundant blast hits from different strains of the same species, for example, E. coli. These hits (can be dozens to hundreds) mask hits from other species which...
View ArticleQuestion About Different Sequence Alignment Programs.
From the following programs, BLASTn, BLASTP, BLAT, PSI-BLAST, MEME, BOWTIE, and ClustalWWhich is the best choice to quickly locate a short DNA sequence in the genome? Which is the best choice for...
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 ArticleBlast W/ G:T Pairing?
I'm using BLAST for a part of my pipeline and need to change my pipeline to allow G/U matching. My google foo isn't getting me very far. Does anyone know if there is a similar version of BLAST with...
View ArticleHelp With Rps-Blast With New Blast
HiI want to make rpsblast with the new blast 2.2.25 with rpstblastn. But I need to format the database. I think for the older blast version you use formatrpsdb and it´s create others files including...
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