Find protein homologs with BLASTp
I'm trying to find homologs of a set of proteins using BLASTp. I'm working with custom databases. I'm using evalue of 0.00001 as threshold. I would like to filter queries having hits with >90%...
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 ArticlePsiblast Warning: Composition-Based Score Adjustment
Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported...
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 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 ArticleError 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 ArticleBlastx Against Swissprot
HiI want to blastx a huge sequnce set against swissprot (as it takes too long aginst nr), is it possible in a resonable time with a regular hardware and how to install and run it locally?Thanks alot!
View Articleblast standalone installation problem
hi, actually i have installed standalone blast. 2.2.30+ version, i followed the instruction they have said,the actual problem came here, it was said that BLASTDB environmental variable will...
View ArticleMethodological process for GO functional annotation of my positively selected...
I did my homework first here and elsewhere but still find it difficult to fit pieces of information I get that would weave a standard methodological workflow enabling me analyze my candidate genes...
View ArticleWhy Do Blastall And Blast+ (Blastn) Give Different Results For What I Beleive...
I've recently run two searches, one with blastall (from legacy blast) and one with modern blastn. Both versions are 2.2.25 (the most recent).The blastall search is: blastall -i test.fasta -p blastn -d...
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 ArticleStrange "Error: OID not found" in NCBI's blastdbcmd
I'm getting a OID not found when executin blastdbcmd. My file is as follows:>cat data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted | grep scaffold00001_37_1_21>scaffold00001_37_1_21 And...
View ArticleIn operons - distinct genes with signficant overlap, or actually same gene?
Hello,I apologize in advance if this question is trivial, I'm very new at all this.I'm trying to do gene comparisons between two strains of bacteria, A and B. When I find a gene in A that doesn't blast...
View ArticleHow To Convert Db Format From Nih Blast To Blat Requirement
Hi I want to run a local BLAT for a huge set of short reads and intend to use BLAT for that. I find that the env_nt db from NCBI is in a different format whereas BLAT requires .fa, .nib or .2bit files...
View ArticleHelp! I Can Successfully Run A Blastp Search In Bioperl But I Want To Also...
I am new to Perl/Bioperl and have run into a problem. How can I perform a blastn search on a DNA sequence? I can successfully perform a BLASTP search, but I can't find any documentation in cpan or...
View ArticleConvert Blast Table With Hsps To Alignment
HelloI have the following BLAST table format output:GRMZM2G5555 GRMZM2G5555 100.00 5197 0 0 2886 8082 2886 8082 0.0 9880 GRMZM2G5555 GRMZM2G5555 100.00 1418 0 0 1 1418 1 1418 0.0 2769 GRMZM2G5555...
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 ArticleTallying Multiple Hits From Blast Results
Hi :)I've been running BLASTs of short sequencing reads against a custom genome. Is there any way I can automatically tally up the number of times an identical/very-similiar sequence read appears?For...
View ArticleWindows Cmd Not Responding With Python Blastall 2.2.17
I'm using the standalone BLAST 2.2.17 with python. However, I'm having a problem with the cmd. When running the script the cmd stops responding at the 15th blast record. It doesn't matter if I change...
View ArticleGene Function through sequence homology
HiSo I've got list of genes putatively involved in Leptospira virulence, and I want to produce hypotheses on their function through sequence homology. So I was thinking of BLASTing them as a first...
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