segmentation fault with SIFT standalone
Hi everyone - I am trying to decipher why I am getting a segmentation fault when trying to use SIFT. I am using the test fasta file, and substituion file they provide. I am using the swissport database...
View ArticleMysterious Lost Version Of Blast (2.2.20)
Some people in my lab use megablast from BLAST 2.2.20 claiming that it is magically faster than the latest.So I went to search for it to see what the difference is:...Deep in the dungeons of NCBI>...
View ArticleMapping blast xml report elements to their variable names in biopython
Hi all ^_^ Im working on a script in biopython that extracts SSR's from some plant species , blast their sequences against each other and group the results of similarity based on some coverage value ....
View ArticleSEED subsystem annotation using blast
Hi,I have performed a BLASTP against SEED database (amino acid sequences). I want to annotate the proteins according to the subsystem. I have downloaded the file subsystem2peg from the seed ftp site....
View ArticleMCL Clustering for Large BLAST output files
Hello,I have pairwise blast result for more than 400 bacterial genome each genome has more than 5000 sequences. I want to cluster the similarity information using MCL to identify protein families....
View ArticleDoes Blast Use Multiple Sequence Alignment
does blast database search use multiple sequence alignment technique ?
View ArticleBlast A Specific Contig Against Multiple Contigs From Another Organism
I have a contig from one organism that is of interest. I have been searching this contig against another organisms complete collection of contigs found on NCBI by using an online DNA translator and...
View ArticleStandalone BLAST with kingdom classification
Hi all,I have an assembled transcriptome from an organism hosting various symbionts and I'm now interested in how many of my contigs hitting to the different kingdoms. What I've found so far is the...
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 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 Articleblastp commandline: against a protein database of a specific organism
Hello,It is a very basic question regarding the -db option. I am using standalone blast+ and I want to blast my query.fasta ONLY against specific organism (e.g human) protein database only. I know...
View Articledownload standalone Blast from NCBI
Hi I am unable to download the standalone Blast (of any version) on my computer and getting ncbi-blast-2.2.30+win64.exe Failed -Network error. Please suggest me some solutions so that i can download...
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
View ArticleBlast Output Into Jsp/Html
I would like to display a blast result in a jsp or html by parsing the xml result of blast without using BioJava? how can I do that?
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 ArticleHow to perform phylogeny analyses
i want to do project on phylogenetics on hiv subtype-1.but how i start the project on this ,what tools are apply on this.
View ArticleHow can I batch a blast for more than 200 proteins at the same time?
Hi everone! I'm a student looking for a tool like greengene.uml.edu whare I can batch a blast of 300 proteins at once angainst ncbi proteins data base. Since greengene doesn't work anymore I'm asking...
View ArticleProblems In Creating Pssm Using Psiblast
Hi, Everyone.Recently I am using PSIBlast to create PSSM.Command seems like this: psiblast -subject oneseq.fasta -inmsa alignment.fasta -outascii_pssm pssm.txtThe problems is Error: NCBI C++ Exception:...
View ArticleBlast Database For Bos Taurus
Hello To All,I want to blast my sequence Only in Bos taurus database Using local Blast (Blast+). But I don't know which database I should use for this from this...
View ArticleParsing Blast Output Biopython Error
Hi, I have the following code def runBLAST(self): print "Running BLAST .........." cmd=subprocess.Popen("blastp -db nr -query repeat.txt -out out.faa -evalue 0.001 -gapopen 11 -gapextend 1 -matrix...
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