Error 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 ArticleHow to create a Blast database of viruses ?
Hi all,For a metagenomic project a want to make a blast database of viruses. I dont want to blast my reads on the entire nt database. But I dont know how to make it. Downloading the result of a query...
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 ArticleBlast Against Pdb Standalone Version
HiI have always used the online service of pBlast and now I am a bit confused since I want to use its standalone version. My aim is to blast a protein fasta sequence against PDB and save all the pdb...
View ArticleHow To Convert Blast Results To Gff
I'd like to visualise the results of a BLAST search in a genome browser. Is there a simple way to get the results in GFF format without having to write a parser myself?
View ArticlePsiblast: Stop After Checkpoint?
Hi,I'm using psiblast 2.2.25+ to generate PSSMs for PSIPred, and I noticed that even after writing to the checkpoint file, it takes a while (feels like half the run time) before exiting, even though I...
View ArticleHow Long Should It Take To Make A Blast Database?
HiI'm trying to install a local copy of polyphen and one of the stages is to make a blastdb from uniref100.I ran this command last night and its still going nearly 12 hours later. I don't know if this...
View ArticleBest Blast Hit Without Pain
Hi,This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to...
View ArticleWhat Makes A Valid Gi List?
Hello all, I cannot figure out what makes a "correct" GI list!Atm I have a list that I produced this using the query below and a awk line to just retrieve the second column values blastn -word_size 11...
View ArticleDownloading And Maintaining A Local, Blast-Able Nr Database
I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with...
View ArticleHow To Show More Blast Results Using Biopython?
Hi,I'm using biopython to BLAST over the internet. However, it only saves 30 results (there are more than 30 results that are under the e-value I chose) in the xml. I've been looking all over but can't...
View ArticleIdentity Cutoff In Blast Output
I was wondering if there is any easy way to do an identity cutoff (e.g. Sequences down to 95% Id) from the blast output locally .I had a look at blastall usage options but haven't seen any flag (or...
View ArticleBlastclust Output Problem.
HI,I have installed the blast standalone latest version 2.2.25 with the help of the installation guide http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html. I ran the blast with a 14Mb fasta file...
View ArticleSequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
View ArticleUse Megan To Parse Sam File
Dear all, I got a question about using MEGAN4 to parsing SAM file. What I want to do is to get taxonomic and functional annotaion of my raw reads against nr database . As the raw reads is too big (11...
View ArticleWhat Is The Difference Between 'Fragment Recruitment' And 'Aligning Reads To...
I have to perform 'fragment recruitment' on my metagenomic reads to generate plots of the percentage identity in the reference sequences. From what I can tell, fragment recruitment just amounts to...
View ArticleBlast Database Size Influence On Number Of Significant Hits
I have a set of gene sequences and specific sequence.cat genes.fa>Gene_1_chr1_1000_1200 ACGT...>Gene_2_chr2_3000_3400 TTAT... cat sequence.fa >Searchable_sequence ACGG... I want to search for...
View Articlehow to find different gene loci between two strains
I already have two complete genome,I want compare them to find different gene loci and related proteins.how can I do that?I read some papers about this,one said use blastp and then COGs,but I don`t...
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 ArticleBlast Query Against Two Different Taxa
Hi,I have a protein sequence which I first do a blastp against NR database without any limitations. It returns a possible protein family and an organism in the output with a very low E-value (something...
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