Which Vertebrate Genomes Available For Blast?
Which vertebrate genomes are available for online BLAST, without the need to download them? There are only a few available through GenBank, more in Ensembl. However, many more vertebrate genomes are...
View ArticleHow To Blast Kegg-Only Data In The 'Nr' Database
Hi there,I dont have a locally KEGG database bought,but I want to Blast my sequences against only the KEGG part of nr db cause you know blast whole nr is really time consuming.Here is my...
View ArticleHow Do I Translate Different Regions Of My Sequence In Different Frames?
What I want to do is say something like in sequence D translate region 1-100 in frame 1 from 102-150 in frame 3 from 160-180 frame -3I would typically extract this information from a blastx table and...
View ArticleMake A Dotplot From Blast Alignment
Hi all,I am a complete beginner with blast. I used the NCBI online service for aligning two sequences, and got a nice dotplot representation. Now I am running blast on my pc, and I would like to obtain...
View ArticleError in run blastpgp
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
View ArticleAlternative to blast, faster but less sensitive?
I am looking for an alternative to blast that can search the UniProt sequence database in a faster way by losing some sensitivity. I am interesting in finding only relatively close homolog sequences,...
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 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 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 To Remove Few Eukaryotic Sequences From Bacterial Sequence Dataset?
Hi I removed the bacterial sequences from a eukaryotic dataset by comparing with bacterial database.As a result there were around 2,000 sequences. But now there are some 20 eukaryotic sequences in this...
View ArticleMethodological process for GO functional annotation of my positively selected...
I did my homework first here and elsewhere but still find it difficult to fit pieces of information I get that would weave a standard methodological workflow enabling me analyze my candidate genes...
View ArticleBl2Seq In Blast+
I have recently installed blast 2.2.24+ and I was looking for the bl2seq tool, but I didnt find it. After some research I found that bl2seq is only found in the legacy blast package. So my question is...
View ArticleAre The Query Strand And Hit Strand From Blastx The Same Strand?
I'm writing code to parse the XML output from a BLASTX search on NCBI's servers, and from this grab from NCBI the nucleotide sequence whose translated protein was found to be a hit by BLASTX . This is...
View ArticleConverting ANY blast output file to an alignment fasta file.
Hey there guys. We use the Blast Command Line toolkit to Blast populations against each other. We created a database of transcriptomes of one population and then used the blast command line kit to...
View ArticleBlast Xml Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
View ArticleForum: The top 100 papers [Nature explores the most-cited research of all time.]
From the article ..... The discovery of high-temperature superconductors, the determination of DNA’s double-helix structure, the first observations that the expansion of the Universe is accelerating —...
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 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 ArticleBlast To Cytoscape
Hi Guys, I am trying to view the results of an all vs all blastp of some sequences with cytoscape. I've been using the Blast2SimilarityGraph app to read in my data (blast -m 8 + fasta file) and then a...
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