Parsing Blast Results In Java
Hey guys, so I am in the process of creating a Java app with a GUI and all based on metagenomic analysis. So my question revolves around running BLAST searches and returning the results in the most...
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 Articleblast -F F equivalent in blast+
In legacy blast there is an option -F, which turns on or off filtering. By default filtering is ON and it effects my results a lot, so I turn it off by -F F (false)In blast+ I couldn't figure out the...
View ArticleNCBI GI to Gene Description
Hello all,I have a very large list of NCBI gene IDs (such as, gi:47221249, ect). I am hoping to use this list to get the descriptions for each of the gene IDs. Using the GI above it would be "unnamed...
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 ArticleHow To Blast A Sequence Against Multiple Databases
Hello,I have downloaded all the chromosome of Bos taurus and I have changed them in blast format using makeblastdb..and now I want to locally blast my sequence against these all chromosomes. now I have...
View ArticleDefault Ncbi Blast+ V. 2.2.25 Parameters
Hi:I'd like to compare my own BLAST tool with NCBI blast+ tool but couldn't find the default parameter of this version. I'd like to know the scoring scheme for match, mismatch, opening gap and extended...
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 Articlehow to find proteins nearest neighbors
Hey all,if I have a protein gi? is there a fast way to find its nearest global structure/sequence neighbor and retrieve top 10/20 hits as protein gi's along with e-value and sequence/structure...
View ArticleBlast - Formatting Output
Hi,I've been using the blastn (version 2.2.28+) standalone tool against a custom formatted genome via:blastn -db BLASTDB -word_size 7 -query input.fa -out filename -perc_identity 100 -outfmt 6...
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Configuring Path To Point To The Bin Directory Inside The Ncbi Folder After...
I can't seem to get Terminal to accept the syntax described on NCBI's help page regarding configuration of the standalone BLAST installation. Here's my syntax and the error messages:
View ArticleError Running Blast2Sam.Pl
I am trting to convert blastn (from blast-2.2.25+) output to sam format using samtools "blast2sam.pl" script.Any suggestions to rectify the error?Error message:Use of uninitialized value in subtraction...
View ArticlemiRNA -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 ArticleTrinity/Rsem/Edger Pipeline...Now What?
HI people,I am a bit new to all of the Bioinformatics but so far I have produced data from the mentioned Trinity/RSEM/edgeR pipeline...I basically have 3 sample condtions -with 3 replicates...
View ArticleForum: How To Correctly Speed Up Blast Using Num_Threads
Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it...
View ArticleNcbi Refseq Viral Genomes
I want to create custom blastdb with all viruses available in the refseq. But I don't know which source files to use. My first point is:ftp://ftp.ncbi.nih.gov/genomes/Viruses/From research I concluded...
View ArticleBlast 2.25+ Segmentation Fault When -Outfmt Set To 6,7 Or 10
Hi all!I am running blast 2.25+ and willing to get output in format 7, setting -outfmt 7. However, with this setting I always get Segmentation fault. Same happens with -outfmt 6 and 10. Other settings...
View ArticleBest Practices/Methods For Developing Bioinformatics Related Web Applications
Hello everybody!I'm planning to transform a few windows programs which I wrote into web applications. Can anybody give me some tips, suggestion or experience with this (Framework, Hosting)? I will use...
View ArticleHow Can I Save A Blast Record (.Xml) Into A Suitable Format For Excel (.Xls)?
I have made a BLAST search through the NCBIWWW.qblast command in Biopython. After having my results saved in a .xml format (by result_handle way, following Biopython tutorial chapter 7) I have parsed...
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...
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