getting error in runing tblastn
Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue...
View ArticleTrouble obtaining chromosome number using standalone blastn
Hello,I'm having trouble obtaining the exact chromosome number, when using standalone BLAST. My current setting is like below:/...BLAST/blast-2.2.29+/bin/blastn -db...
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 ArticleFind The Rid For A Remote Blast+ Result
I ran a remote blastn search using the command line blast 2.2.25+ and got the results back in asn format. when I went to reformat the results using blast_formatter, I realized I needed the RID for my...
View ArticleBlast Text-Output To Xml Converter
Hi, I'm looking for simple way of converting blast output in text (stardard output) into XML format (maybe some has got script?). I've looked elsewhere but couldn't find anything:/UPDATE I ended up...
View ArticleNo Alignment In The Output Of Blastn
Hello everybody, I am trying to BLAST a nucleotide query against a nucleotide database via command line.The problem is that, when I try blastall -p blastn -d mydatabase -i myquery I get just:BLASTN...
View ArticleFinding Coordinates Of Genes In Genome
Hi GuysI think I have a very trivial question. I have a multi-fasta file of rRNA genes. I need to find their location in the genome. It will be easy to blast them but not sure how can I extract the...
View ArticleHow To Get Conservation Of Vaccine Candidates Between Hundreds Of Bacterial...
Hi community,We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains (about...
View Articlewhat should be the query coverage for miRNA 21nt query sequence against the data
what should be the query coverage for miRNA 21nt query sequence against the ESTs, for further proceeding those ESTs for secondary structure prediction.I am getting good E- values around 0.01 to 0.1....
View ArticleOld BLAST data
Hi,I am currently developing a tool that compares the result of one BLAST search against different versions of a database to explain why some conclusion/finding comes up at one point but not at...
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 ArticleBlastx With Xml Format
Hi all, I'm currently using standard alone blast, the version is ncbi-blast-2.2.25+. I tried to made xml format blast result for my downstream analysis, but I had some problems in generating it. The...
View Articleblastn -no_greedy switch
Does setting the -no_greedy switch make blastn behave like Smith-Waterman? The documentation states that the switch allows blast to "use non-greedy dynamic programming extension". It isn't clear to me...
View ArticleHow do I generate the correct input files for Blast2GO from CuffLinks2 output?
Hi everyone,Sorry if this is a "no-brainer" type of question, I just started assembling my first transcriptome last week (and am having a really good time learning how to work with all these data!). I...
View ArticleWarning Unable To Open .Nin
I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux. I created the database for Bos_taurus using Formatdb commamd of...
View ArticleLocal Graphic View Of Blast Results
When I do local BLAST with the parameter -m 8, I find that one query sequence can match the same subject sequence at several parts. I wonder if there is some tool that can read the BLAST m8 output and...
View ArticleAlmost Nothing Mapped Using Bwa Or Bowtie. But A Lot Of Mapping In Blast
I have pair-ended illumina samples with the read length of 100-150bp. I tried to map them to the reference genome/transcritpome, but almost nothing mapped using BWA or Bowtie.When I blast them to nt...
View Article[Help]: Extracting Sequence From Fasta Using Blast Informations?
Hi there! This is my first post on your forum and I hope you'll be able to help me. This is my first intership in bioinformatics and I'm kind of learning everything by myself. I learnt how to use...
View ArticleGenerating Protein Consensus Sequence For Blast Input
I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database.how should I go about it?
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...
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