Strategies To Blast Against Fastq Files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View Articleproblem running local blast after downloading on MacOSX
Am newish to linux but very familiar with BLAST and I need to use BLAST locally through command line on my MacOSX (Yosemite)I downloaded the BLAST+ using ncbi-blast-2.2.18+.dmg installer and following...
View ArticleAn Error By Using Ncbi-Blast-2.2.25+ (On Windows)
Hi all I downloaded blast+ software package (for windows), and installed like theBookshelf; to run it i used this "ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out...
View ArticleSome Problems In The Result Using All To All Blast In Blast 2.2.25 (Windows)
Hi, everyone. i got a problem when i run local blast in the all to all way(the subject library is identical to the query sequences.) i just was confused by the result. The alignment length is much...
View ArticleWhat command generate blast database from file in all.fna folder?
I downloaded genome of Bacteria, which file name is all.fna.tar.gz from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/. Next I extract file I got folder all.fna. I want to generate all bacteria...
View Article[Fastacmd] How To Retrieve Sequence From Blast Db
Let's say I have multifasta with protein sequences having internal IDs (integer)>1234 MGKL...*I build blast db using:formatdb -i infile.fa -pF -n someDBBut then, I'm unable to retrieve sequence from...
View ArticleWhat Substitution Matrices Are Available For Blast?
I'm having trouble locating documentation on what substitution matrices are supported by command-line BLAST+ tools. Do they have a specific set of matrices built in? Are they hidden in a directory...
View ArticleFinding Protein Homology?
I'm looking for something that's more rigorous than BLAST and less rigorous than a global alignment-esque algorithm. Is there a paper out there that compare methods? What's the most popular method?I'm...
View ArticleBl2Seq With Multi Fasta
Hello,I have two groups of sequences in separate files (1.fasta and 2.fasta). I need to make comparison between them. However I cannot runbl2seq -i 1.fa -j 2.fa -p blastp -o outputbecause bl2seq is...
View ArticleProblem Running Blast Jobs.
I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequences each.For all jobs except the first one blast returned an error:blastall(7004) malloc: ***...
View ArticleAnnotating sequences after de-novo Trinity assembly and RSEM analysis...there...
Hello, I'm hoping someone can provide some insight or point me in the right direction... I have very little programming knowledge and am fairly new to RNA-seq but I'm sure there must be an easier way...
View ArticleHow To Define And Calculate Cip ( A New Parameters For Blast Analysis Of Cip...
IN the paper “Improved criteria and comparative genomics tool provide new insights into grass paleogenomics " they said:To increase the significance of inter-specific sequence alignments for inferring...
View ArticleFinding Lincrna Alignments With Blast Versus Blat
Hello,I have a lincRNA sequence (XLOC) that I retrieved from the Broad Institute. When I BLAT the sequence against the human genome, I get a 100% match and it aligns with the correlating transcript...
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 ArticleDatabase Error When Running Blastn
Hello, as initially stated here, I am experiencing problems when I try to run the blastn command blastn -query myquery -db mydatabase.fasta.nhr.What I get is:BLAST Database error: No alias or index...
View Articleblast output for FASTA (aligned sequences) to get organism name
Hi,I want to get the organism name from blast output (FASTA (aligned sequences)) for the specific protein.I am a beginner in python. Please help me to write the script for getting organism name in...
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 ArticleMakblastdb And Low Complexity Regions
Hi i want to create a blast database from sequences that under blast are marked as "low complexity", is there a way to make makeblastdb turn off this filtering?i'm aware that the sequences might be...
View ArticleProblem with NCBI-BlastN
Hello, I have recently reinstalled the OS of my workstation, changing from Fedora to Ubuntu. I then proceeded to install ncbi-blast (in its 2.2.28 version), but oddly when I try to run a job, it only...
View ArticleNcbi Non-Redundant Dataset (Nr) In Protein-Blast To Look For Homologs?
Hi all,this must be very basic, but still. I have a protein sequence for which I want to find homologs. I go to BLAST and do, for simplicity here, a regular BLASTp.I know that blasting against...
View Article