Multiple mapping (Taxonomy, Seed, ...) of blast(-like) tabular output
Hello, I am dealing with short sequence reads (>1,000,000 reads) from a metagenome and a metatranscriptome. I used a BLAST-like program called RAPSearch 2, which provides me with a BLAST Tabular...
View ArticleParsing 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 ArticleBlastx Against Swissprot
HiI want to blastx a huge sequnce set against swissprot (as it takes too long aginst nr), is it possible in a resonable time with a regular hardware and how to install and run it locally?Thanks alot!
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 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 ArticlePreview temporary outputfile blast
Hi, Is there a way to peek at blast temporary file? I would like to know what sequence is analyzed in order to foresee how long the program will take to finish. top command shows that it uses around 4...
View ArticleWhat Exactly Does Formatdb Do?
As far as I know, the blast searches for homology in the way that indexing query(word list), scan database(automaton), extension and so on. Then why should we pre-process the database with formatdb.I...
View ArticleTallying Multiple Hits From Blast Results
Hi :)I've been running BLASTs of short sequencing reads against a custom genome. Is there any way I can automatically tally up the number of times an identical/very-similiar sequence read appears?For...
View ArticleQuick Command To Split Large Blastx Files?
Any thoughts? I have large 7 gb files as resulted from Blastx any clue how to split them?Edit:These are standard blastX files (fasta). I need to split them for a program (binning) call SOrt-ITEMS/MEGAN
View ArticleParse Blast Output ..
i want to parse this blast output but compilers giving NULLPOINTEREXCEPTION .. input file and source code of java program is given below ... plz help me out..Exception in thread "main"...
View ArticleNcbi Blast Command Line Align Two Sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
View ArticleIs there a good service for annotating transcripts?
After getting say 100k transcripts from an rna-seq project, generally one wants to annotate them against a database like nr, using say blastx. Problem is, this is very slow, taking e.g. a week with 24...
View ArticleClassify Or Align ?
Hi, I am working with a bunch of microbiologists which with I conduct metagenomic analyses. In the past (not so old), I did my PhD thesis on Bayesian Network classification (a supervised classification...
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 ArticleMakeblastdb Help
Hi,I feel I'm being really dumb here, so please excuse me! I have a file of fasta sequences which I want to make into a blast databse for standalone blast.I haev the fasta file saved in the bin folder...
View ArticleI Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found...
This is the errorBLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/aj3/Desktop/h/database::]what should I do? do I have to use any other commands...
View ArticleBiopython: Executing Blast On Custom Db
Ok, so I am using the NcbiblastxCommandline wrapper to execute a BLAST search on a custom database. cline = NcbiblastxCommandline(cmd='blastx', query=temp_path, out=blast_path, subject=path, outfmt=5,...
View ArticleBlast Error: Tax database file not found
Hello, I am running this command for a blast search.blastx -query Ndiv_cap300.fasta -out Ndiv_run -outfmt 7 -db nr -num_threads 32 -evalue 1e-3 -max_target_seqs 5however I get the following error that...
View ArticleDistribution of e-values in Best Reciprocal Blast Hits for Ortholog Mining
Does anyone have an idea of how the distribution of expect values will look when using reciprocal blast to detect orthologs?
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