Any Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View ArticleProblem using a custom blast database in tblastx
Hello. I tried to create a custom DB for blast. I downloaded fasta files from NCBI from an SRA project and then run this command makeblastdb -dbtype nucl -in sra_data-DB.fasta -input_type fasta -out...
View ArticleForum: Looking For Help To Understand Bioinformatics Papers On Blast, Yasara...
Hello, I'm a student and i've got to make a paper about bioinformatics i've been working on it for a while and i'm almost done. I only have to write about BLAST, YASARA and the huntington disease...
View ArticleAlternative To Local Blastplus To Blast 10000'S Sequences On Nr, Swissprot...
Hi,Here is a case scenario that happens quite often to me: I need to blast from 1,000 to 20,000 sequences in order to find the proteins these sequences code for. These sequences come from fish cDNA...
View ArticleRunning Blast For A List Of Pairs
Hi,I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?I tried bl2seq but unfortunately it does not produce the alignment of the whole...
View ArticleHow To Make Pssm With Makeblastdb
i want to make a pssm from a fasta file for searching with rpsblast, i have the 2.2.23+ version of blast, so formatdb is replaced with makeblastdb. I have used it to make a database from the genome im...
View ArticlePerforming Blast/Smithwaterman Searches Directly From My Application
Bringing in my questions from stackoverflow:I'm working on a small application and thinking about integrating BLAST or other local alignment searches into my application. My searching has only brought...
View ArticleBlast 2.25+ Segmentation Fault When -Outfmt Set To 6,7 Or 10
Hi all!I am running blast 2.25+ and willing to get output in format 7, setting -outfmt 7. However, with this setting I always get Segmentation fault. Same happens with -outfmt 6 and 10. Other settings...
View ArticleHow To Extract Desire Genes Blast Xml Result From A Big Blast Xml File
Dear community, I have a XML file contained 50,000 genes Blast result with 10 hits for each gene. I want to mine desire genes Blast result from that XML file and the output file is still in XML format....
View ArticleHow To Search Blast With Ensg Id'S?
I have some ENSG id's and I would like to search BLAST database with this id's. When I use the ENSG id's directly, BLAST cannot find any genes. I think I need to convert the ENSG id's to some other...
View ArticleHelp With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast)
Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code...
View ArticleBlast: Homology Or Similarity?
Hi Biostars, I am having a dispute with a reviewer. Is BLAST a Homology or similarity based search? thanks EDIT The BLAST is performed against a custom DB containing only homologous proteins.
View ArticleRemote blast+ skipping query sequences
Hi, I'm running a remote blast on the nr database using some contigs I've assembled and I've noticed that it is skipping many contigs. Here's the command I'm using to search:time blastx -db nr -query...
View ArticleCan Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline...
Hi, I would like parse the XML output of a local psiblast (NcbipsiblastCommandline wrapper) by putting the stdout from the wrapper into a python string variable and then using NCBIXML.parse to parse...
View ArticleStandalone blast results wrong
Hi,I downloaded the NR database from NCBI about 2 months ago. The past few times I have run a blast search on some contigs, the results have been wrong on many of the query sequences. I checked this by...
View ArticleEmbedding Blast Tool In A Website
I'm planning to include BLAST search tool in a website to search against my own databases where user can choose one of the two databases with all the optional blast parameters (e.g. E value cutoff,...
View ArticleBlast 2.2.24+ Database Error
When running local BLAST on a big database (all human proteins) I get the following error:proteinsApplicationError: Command 'blast-2.2.24+/bin/blastp.exe -query "query.fasta" - db...
View ArticleHow Can Different 3 Reading Frames Have Similarity For The Same Sequence...
Hi, I have a DNA sequence ( it's about 388 bp), which I am comparing with GenBank sequences using Blastx. I understand that Blastx looks into all possible 6 reading frames when translating a DNA seq,...
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...
View ArticleHelp With Formatdb And Blast All
I have my own database of sequences stored in MySQL. I convert this database into a blastable format using formatdb, code below:formatdb -p T -i db.fastaI then do the same with the query sequence and...
View Article