assigning function to putative/hypothetical proteins
Hi All,What is the best and current bioinformatics approach to assign functions to putative/hypothetical proteins?Thanks
View ArticleBlastdbcmd - Too Many Positional Arguments , The Offending Value: %F - Windows
Hey guys, I'm trying to use blastdbcmd - when I type the following on cmdblastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txtthe following error pops up:Error: Too many positional...
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 ArticleLimit The Memory Size Of Blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
View ArticleFind Mismatch And Gap Positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleWhich 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 ArticleFormatdb For Chromosome Database?
Hi,I recently downloaded the new Fugu v5 assembly database from IMCB (http://www.fugu-sg.org/downloads/downloads3.htm). This is my first time using a chromosome level database (I am used to contig and...
View ArticleBlast Short Sequences Containing Repeats
I try to detect repeats using blastn. I use the same sequence as query and subject. The sequence contains a 21bp tandem duplication. I expect three hits: The whole sequence aligns itself.First...
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 ArticleOnline Tools To "Prettify" Blast Output
Can anyone suggest an online tool, for a non-bioinformatician (not for me you understand, oh no not me), that will make BLAST output "pretty", i.e. add shading to make mismatches and so on more...
View ArticleBlast+ On Windows
I need to compile blast+ on windows.Can someone tell me how do i do this.I tried Visual studio 2010,but i get an error saying that some project tree builder is not found.I am a beginner so please be a...
View ArticleHow To Concatenate/Merge Blast Xml Outputs?
I process my blast (BLASTN 2.2.26+) searches through a script that divides the fasta inputs into N pieces, distributes one blast instance for each piece (in N processes), and, once over, concatenates...
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 ArticleEmbedding Blast Tool In A Website
I'm planning to include BLAST search tool in a website to search against my own databases where user can choose one of the two databases with all the optional blast parameters (e.g. E value cutoff,...
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 to recreate alignment information from TSV output
Hi,I have obtained BLAST output file in TSV file format which looks like - # BLASTN 2.2.29+ # Query: SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2 # Database:...
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 ArticleIdentifying Viral Sequences In Next Generation Sequencing Data
I am attempting to find viral sequences in the RNA seq data of sequenced tumors. Currently I have changed bam files into fasta files and have used the refseq viral dataset from NCBI, formatted it as a...
View ArticleIs There A Query Parameter For The Online Blast That Would Filter For Hits...
Hello,I am running blastn, blastx and tblastx searches on NCBI's nt, est, nr and HTGS databases using transcriptome data containing ~56,000 contigs. I have been able to produce biopython scripts to run...
View ArticleBio::Tools::Run::Remoteblast Settings
I'd like to perform a blastn on the NCBI servers using Bio :: Tools :: Run :: RemoteBlast. No problem to configure "standard" parameters as defined here.My problem is with more exotic setting such as...
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