How To Get Conservation Of Vaccine Candidates Between Hundreds Of Bacterial...
Hi community,We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about...
View ArticleIdentify Contamination With Blast
Many reads from a recent RNA-seq sequencing run I had done are not mapping to the reference sequence they had come from. I converted some of the sequences to fasta format, and blasted them against NR...
View ArticlePython/Perl Script For Defining Minimum Coverage Of Blast Match
Hi - does anyone know of a script that allows for a blast result to be filtered by the minimum total coverage of the query/subject that the alignment/s represent?I'm imagining a script that calculates...
View ArticleRepeatmasker Crashes Before End Of Run With "Can'T Fork..."
I've been trying to run RepeatMasker but it keeps crashing with the error "Can't fork...". In the RepeatMasker script source code, this is here:FORK: { if ( $pid = fork ) { $flag = 1; waitpid( $pid, 0...
View ArticleHow Does The Blast Algorithm Work ?
hello could someone please point me to some article that explains how the blast algorithm works.
View ArticleAre Alignment Lengths Reported In Ncbi Blast+ Results Counting Nucleotides Or...
Very simply, what are the units of the alignment length reported by BLASTX and BLASTP? The units of length are not listed in the output column headings (-outfmt 7) and I have found nothing in the...
View ArticleDownstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
Are there any good available programs/scripts for analyzing assembled transcripts? I imagine something like a script to blastn, blastx and tblastx each transcript and report the best hit. Something...
View ArticleBlast2Go Memory Allocation
I'm running BLAST2GO on a Linux (Ubuntu 10.04 32 bit) machine with 24 GB RAM (8 processors). No matter what I specify for the maximum memory, it only allocates 455 MB RAM, which is not enough for the...
View ArticleCustomize 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 ArticleWhich Bioperl Module Can I Use For Parsing/Mining Blast Output?
Hi to all, I have blastx results (default output). There are some blast hits starting at frame 1, others starting from frame2,frame3, frame -1 etc. I want to collect all query IDs that blast in...
View ArticleHelp In Standaloneblast Bioperl
Hi, I am new to bioperl. I have been trying to run blast, I get my blast output, I am not sure, how to use $factory in bioperlI have blast installed and has been added to my PATH variable.use...
View ArticleHow Is The Score And E-Value Calculated In Blast Outputs
Hi!I am working on a BLAST similar tool and wanted to implement the Score (raw Alignment score) and the E-value. I was wondering if someone could please explain me how it is calculated by showing it...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleHow Can I Download The Results From An Ncbi Blast Search?
I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download...
View ArticleWebtool For Fetching Pmids From Blast?
Hi, I was wondering if there is a web service that extracts all of the PMIDs that are in the results for a BLAST search? Example: I input the sequence for enchanced FLP and get a list of all the PMIDs...
View ArticleShortlisting Genes From Various Gene Prediction Methods Based On Blast Results.
Hey Folks, Background: I am trying to shortlist the list of genes predicted by different gene prediction methods. For this i am considering blast hits as my basis for shortlisting. I merged the results...
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 ArticleMakeblastdb And Blastx
Hi, I tested the makeblastdb and blastx but doesn't seem working for me. Can you please check if I did anything wrong?I used 2 fasta sequences (SETREF : testDB.fa) as a reference and a file with...
View ArticleMining Ortholog Cliques
Does anyone have experience working with mining cliques from ortholog data? I have orthologs generated by best reciprocal blast from 22 species. It is 21 Ensembl species with one species we are...
View ArticleWhat Program Or Database To Use To Analyze Blast Result Output?
Hello, I ran the blast locally and got the blast output like followingquery1 gi|4003386|dbj|AB020866.1| 98.44 64 1 .. query2 gi|60834728|gb|AY894071.1| 92.11 76 2 ... query3 gi|21618453|gb|BC032801.1|...
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