error downloading refseq for local BLAST install via FTP
I am having trouble downloading the refseq database required for BLAST+. I am following the instructions from http://www.ncbi.nlm.nih.gov/books/NBK52640/ but get No such file or Directory error using...
View ArticleOld Blastall Vs New Blastall
I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new computer. I wanted to test the new version of blastall with a lamprey genome database and sequence that works...
View ArticleGene ID conversion and Pathway analysis after mosquito blast
Hi all I have got my blast result from mosquito Contigs Fasta format. Sth like query_name query_length accession_number 1059N_ae_contig_1 676 XM_001650645 1059N_ae_contig_5 563 XM_001650988...
View ArticleDownloading Fasta Files
i need to download about 40 complete genomes from ncbi and still filter out sequences between specified bps(like btn 1000bp to 3000bp) from the genomes separately. i need help on how to do that. i...
View ArticlePreview temporary outputfile blast
Hi, Is there a way to peek at blast temporary file? I would like to know what sequence is analyzed in order to foresee how long the program will take to finish. top command shows that it uses around 4...
View ArticleSequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
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 ArticleCommand to get BlastDB(Blast Database) information
Hi guys, I have a very simple question on how to get the information on the size of BLASTDB created using standalone BLAST. I have created several BLAST databases and now I need information on their...
View ArticleBlast Nucleotide Vs. Nucleotide, Plus-Minus Results Only
Hi Folks, I am interested in running a blastn search to search for complementary sequence (potential biological function) between two groups of sequences, (Query blasted against Reference) such that...
View ArticleCompare Two Protein Sequences Using Local Blast
Hi,I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools....
View ArticleRunning BLAST on huge files
Hello,I have quite a simple question.I have a huge file of 7 GB (approx. 43 million sequences). I want to blast my 1 sequence (1000 bp) against it. Is it possible to do it on a normal computer with 300...
View ArticleError with database alias when running blastp
I have made a blast protein database with this command:./makeblastdb -in input.fsa -out prot.db -dbtype prot -hash_indexIt has generated 8 files as follows:prot.db.phd prot.db.phi prot.db.phr...
View ArticleErrors In A Bioperl Script, Please Help Me To Have A Check, Thanks In Advance!
Dear friends: I have a blast report, and want to extract following information for each result(query): the Query_name, hit_number, name and description of the hit(HSP) with the highest identity. my...
View ArticleHow To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens...
I used PSI-CD-HIT-2D to compare the proteome of pathogen A to pathogen B from the same genus at 30% identity. The matched protein sequences (homologs above 30% identity) are then compared again to...
View ArticleHow To Concatenate Blast Results (M8) Via Setting Threshold Of Distance...
hi, dear guysI performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance. however, these hits have no...
View ArticleCan Biopython Parse Gzipped Xml From Blast?
I have been using blast+ with the xml output format (-m7 in the older days, and outfmt 5 with ncbi-blast+). Since the XML files are huge, I have been gzipping them. I have also been using Biopython to...
View ArticleFrom Blast To Ucsc Genome Browser: Valid Loci
Hello,BLAST, sometimes, does not propose direct links to Genbank pages as reports, and this leads to unaccepted entries in the UCSC Genome Browser's search term box. How could I avoid those results? Is...
View ArticleWhat is the best approach for predicting regulatory elements in the pig genome
Hi All,What is the best computational method for predicting regulatory elements in the pig genome? I have a list of differentially expressed genes as determined by RNA-Seq in 3 different tissues and I...
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 ArticleBlast: Influence Of Database Filesize On Performance, And Purpose Of...
Obviously BLAST is going to have better on-average performance on a smaller database than on a larger database. But for a particular (large) database (let's say 10s of GB), how does splitting up the...
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