An Alternative To Blastx With Speed Similar To Bowtie
Hi,Is there any fast aligner that aligns nucleotide sequences to protein databases?I've used blastx but blastx is too slow and takes too much memory, I'm wondering if anything like bowtie exists.Thanks!
View ArticleWhat does sframe signify in BLAST output?
Hi,I am relatively new to the field of Bioinformatics and have just been introduced to BLAST. I'm trying to understand the output available from the BLAST program. As listed in the NCBI manual, I am...
View ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleCreate Blast Database From Query Result?
Possible Duplicate:make a custom BLAST library using the output of another blast result Hello, I would like to create a BLAST database using as input a file generated after executing a BLAST query. I...
View ArticleProblem With Interpretation Blast Results
Hi, I'm struggling with BLAST. I'm not sure if I can properly interpret the results of BLAST. Can anyone tell me when I can be sure that the sequences of the proteins are enough similar to be...
View ArticleTool to map sequences and get genomic coordenates
Hello, Is there any software to map sequences against a genome and get genomic coordates/genomic ranges? I used several tools to get short sequences of ncRNA, but in the process i lost track of the...
View ArticleHow To Force Blastp To Display All The Possible Combination Of Alignments?
I want to use blastp to find out all the alignment among two fasta file.Here is my command:blastp -query "A.fasta" -subject "B.fasta" -evalue 1 -outfmt 6 > output.txtI have already set the e-value...
View ArticleHow To Get Status Update In Ncbi Standalone Blast?
For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server. I am not getting any status message like 15 of 100 sequence is running. Is it possible to get any...
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 ArticleIs A "Gene-Like," Returned By Ncbi Blast, Indicative Of Gene Family Membership?
I'm looking to sequence HSD in a non-model organism. I've been using degenerate primers for awhile and finally got a successful sequence. BUT when I enter it into BLAST, I get high sequence identity...
View ArticleIs Blastall Only Using Blast, Not Blast+?
Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.
View ArticleRunning A Standalone Batch Blast With Fasta File Using Perl, Can'T Get...
I'm running standalone blast locally. My blast query sequencess are in a fasta file called human_seqs.fasta, which comprise around 300 sequences. Being blasted against a much larger database called...
View ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View Articlepredict binding affinity
Hi all, If I know amino acid sequence or nucleotide sequence of a ligand and that of a receptor, can I predict the binding affinity between the ligand and the receptor? What is the state-of-art program...
View ArticleBlast Results: Xml Tags Explained ?
Hi there,I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .More precisely, I...
View ArticleError in run blastpgp
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
View ArticleBamfile Coordinates
I blasted a gene sequence against a whole genome and found out that the subject start site:31636628 is higher than the subject stop site:31626793. I need the coordinates to excise a portion of a...
View ArticleBLAST: Querying a single sequence without input file in C
This is with reference to the query posted in https://www.biostars.org/p/17265/. If I try to run the following using command line it runs perfectly fine: blastn -query <(echo -e...
View ArticleAnnotating Rna-Seq Data Using A Reference Genome.
I have RNA-seq reads from a non-model organism. I used cufflinks to identify transcripts. Is there an existing pipeline to BLAST these transcripts to a model organism's proteins to identify orthologs?
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