miRNA -identification animal
Currently I am predicting miRNA in animal.. when I perform BLASTx, i dont know how to select the non-coding protein? plz help me.. Do we have any other softwares or tools to remove coding protein??
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 ArticleIdentification Of Promoters From Gene Sequences And A Vertebrate Genome Assembly
I have a number of genes which I'd like to locate in a whole-genome assembly, in order to identify the genes' promoters. In the past I've done this manually using BLAST and BLAT, which has worked well,...
View ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleBlastall gives several hits to the same subject sequence
Short query sequences will sometimes give several hits to the same (often large) subject sequence. This is problematic if you ask for the 20 best hits since blastall will actually give you the best...
View ArticleMultiple Blast Output Formats From 1 Blast Run
Is it possible to generate 2 different output formats (tabular and the default one) by running blastn just once or I have to either1) Run it 2 times - one for each desired output2) Generate the tabular...
View ArticleHow Could I Run A Huge Number Of Blast Calls Faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
View ArticleEquivalent Blast And Blast+ Commands
Hi all,I used to use an old blast version (2.2.21) and now I'm moving to the latest blast+ version (2.2.25). The thing is I don't know which options in the 2.2.25 version are the options equivalent to...
View ArticleBlast Text-Output To Xml Converter
Hi, I'm looking for simple way of converting blast output in text (stardard output) into XML format (maybe some has got script?). I've looked elsewhere but couldn't find anything:/UPDATE I ended up...
View ArticleBlast Against Sra Dataset
Dear all, I have downloaded a number of SRA genomic seqeunce datasets. I am wondering if it's feasible to perform BLAST againt these datasets using a number of gene seqeunce. This analysis will...
View ArticleBlast E-Value To Database Size
Hi,I'm thinking of splitting the database to smaller chunks. And, blast my sequences against them each on a separate process. My only concern is the results (which I will merge later).Would the...
View ArticleAre old versions of NCBI's nr stored somewhere?
Hello,I'd like to study how NCBI's non-redundant protein database (nr) has developed over the years. However, I'm yet to find a way to download anything but the latest release from the NCBI ftp. Are...
View ArticleUsing Blast From Within Perl.
Hi all.I recently installed the latest version of Blast (standalone) on a Win XP machine and altered the appropriate path settings, i.e., C:\blast\bin. Having searched the web for an example of using...
View ArticleNcbi Web-Blast With Huge Subject Sequence Provided By The User In Fasta File
hello everyone,I tried to blast my query sequences with my subject sequences in fasta file...i uploaded both my query and subject sequences in fasta file to the ncbi blast page, but it didnot...
View ArticleHow I Can Find The Sequence For The Gene That I Want To Synthesize?
Hi,I'm starting with bioinformatic, and i want ask u this question:I have this sequence: vpnvrgmgar davylmekrg ikvritgrgr vieqslapgd kikngmqcsl rlg from "penicillin-binding protein dimerization domain...
View ArticleConcatenating fasta files for BLAST
I have two fasta files from WormBase. One is the coding transcripts, the other is ncRNA. When I BLAST (using NCBI Blast+) 44k 60-mers against just the transcripts, I get 37,216 hits. When I...
View ArticleBlast Results: Xml Tags Explained ?
Hi there,I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .More precisely, I...
View ArticleFormatdb And Non Coding Characters
Dear BioStarI want to use a non coding character, eg X to process snp data. The X helps me to find the snp position in blast hits. However, when I format the blast database from a fasta file containing...
View ArticleHow can we find mature 3p sequence in precursor miRNA through insilico mining
How can we find mature 3p sequence in precursor miRNA through insilico mining.......? eagrly waiting for answer expecting helping hands
View ArticleSome Problems In The Result Using All To All Blast In Blast 2.2.25 (Windows)
Hi, everyone. i got a problem when i run local blast in the all to all way(the subject library is identical to the query sequences.) i just was confused by the result. The alignment length is much...
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