How To Automatically Screen Thousands Of Sequences Using Vecscreen
I looked at the NCBI Vecscreen website (http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html), and you can put multiple sequences in fasta format in at a time. It allows you to download results, but...
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 ArticleBlastp With Just Top Result From Each Organism
(My first Q on biostar, forgive any transgressions please!)I would like to blast a protein/aa sequence and filter(?) my results to include only the top result from each organism. I'm keen to use R or...
View ArticleFormat Uniref90.Xml To Database For Blast
we want to get a formated database for BLAST from Uniref90. we referred an article which used an early release Uniref90, say version 10.0 ftp.uniprot.org only provide the XML format of this version....
View ArticleComparing two or more genomes for novel regions
Usually blast search looks for similarities. How about looking for unique regions among several genomes. Is it possible? How to do it? I found the pan-seq to find novel regions among bacteria. How...
View ArticleNcbi Wgs/Nt/Env-Nt Databases
I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was...
View ArticleSEED assignment (MEGAN5)
For me it is not clear how MEGAN assign the SEED classes to the sequences. In the manual, it says that it is made throughtout the identification of RefSeq id (accession number?). When I load my blast...
View ArticleOutput File Format "6" - Blastplus - Gene Name ?
I am working on a second design for a sequence capture array (similar to a micro-array, but with genomic DNA) and I want to blast a few sequences that seem problematic in my design. The sequences are...
View ArticleNCBI GI to Gene Description
Hello all,I have a very large list of NCBI gene IDs (such as, gi:47221249, ect). I am hoping to use this list to get the descriptions for each of the gene IDs. Using the GI above it would be "unnamed...
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 ArticlePython Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleBlast Runs In Unix Shell But Not Perl
I'm trying to run BLAST in Ubuntu 12.04, using a virtual box. It works fine in the command line, and produces the appropriate results using this blastn -query myfasta.fna -db nt -out output.outWhen I...
View Articleclustal w result interpretation
I used microrna in clustal w software to remove redundancy . some part of output was like this ..can any one tell how to interpret the results ..... what is that score. how can i know wether the...
View ArticleTaxonomy Of Blast Hits
Lets have 200k genomic contigs with some (unknown) bacterial contamination. I blasted (blastn vs nr) all of them, got tabulated output and passed the uniq acc nos ca 5k to Batch Entrez. Since neither...
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 ArticleBlast/Reblast To Verify Homologies
Hi!I am an informatics student from Germany attending a practical course on bioinformatics. I am new to the field of bioinformatics but I am willing to learn a lot. My first task is the following: I...
View ArticleRepeatmasker Crashes Before End Of Run With "Can'T Fork..."
I've been trying to run RepeatMasker but it keeps crashing with the error "Can't fork...". In the RepeatMasker script source code, this is here:FORK: { if ( $pid = fork ) { $flag = 1; waitpid( $pid, 0...
View ArticleRepetitive element coverage of consensus
I have a consensus sequence for a class of repetitive elements (from repbase) and I want to find out the depth coverage of the real genomic instances (taken from ucsc rmask table) against this...
View ArticleHow To Merge Fasta Header With Description Using Perl :
I have a fasta file that contains sequences like so :>PT_TAC_1 ATGCATGCATGC>PT_TAC_2 ATGCATCGATCGFollowing BLASTx, i obtained blast results in tabular format. The Sequence ID is in one column and...
View Articletblastx in blast+ gives an error regareding a DB alias but blastall works fine
I'm trying to run `tblastx` locally. For this I created my own database using the command: `makeblastdb -in all_seqs.fasta -dbtype nucl -title "my_db" -out my_db -hash_index -parse_seqids`Then running...
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