Blast For Cygwin?
Which version of BLAST is prepared for Cygwin?I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed,...
View ArticleHow To Make A Blast Database With Taxonids From Ncbi Query.
I am seemingly stuck with something that should be very simple and I hope I haven't overlooked something obvious. Question: How can I make a valid Blast-database with Taxids from a NCBI query export?...
View ArticleHow Can I Batch Blast Sequences To Identify Them?
I have a list of 189 Accession numbers for 16s rRNA, how can I batch BLAST these to find which species they are closest too? I tried this server: http://greengene.uml.edu/programs/NCBI_Blast.html but...
View ArticleHow To Find Sequences With A Given Number Of Mismatches
Hi! Is there any script or tool that allows to find similar sequences given the maximum acceptable number of mismatches? What I want is something similar to a Blastn search, but instead of filtering...
View ArticleFinding Protein Homology?
I'm looking for something that's more rigorous than BLAST and less rigorous than a global alignment-esque algorithm. Is there a paper out there that compare methods? What's the most popular method?I'm...
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...
View ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
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 ArticleScript To Submit And Manage Blast Jobs On A Cluster?
Hi,I make use of a local cluster (managed through LSF) to BLAST large sequence sets. I wrote a basic script to split a fasta file and submit each part as a different BLAST job. Does anyone know of such...
View ArticleBlast Display Non-Matching Ends Of Sequence
Is it possible for blastn to show the parts of the database which do not match? Eg if I ask blastn for matches to a 36 base pair sequence and it finds a human DNA sequence which matches 27 bases of 30,...
View ArticleBest strategy to get GO terms for a proteome?
Hi,I would like to know the best strategy to get the highest amount of GO terms for the bacterial proteome I'm working. Since it's a non-model organism, I will build the GO database from scratch.I...
View ArticleIs There A Query Parameter For The Online Blast That Would Filter For Hits...
Hello,I am running blastn, blastx and tblastx searches on NCBI's nt, est, nr and HTGS databases using transcriptome data containing ~56,000 contigs. I have been able to produce biopython scripts to run...
View ArticleBamfile Coordinates
I blasted a gene sequence against a whole genome and found out that the subject start site:31636628 is higher than the subject stop site:31626793. I need the coordinates to excise a portion of a...
View ArticleBLAST against subsets selected from within UniProt
I want to perform a BLAST seach and see the alignment results only against a small set of sequences either selected from within UniProt, or a list of IDs mapped in via the interface upload. If anyone...
View ArticleHow Could I Run A Huge Number Of Blast Calls Faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
View ArticleHow to identify transposons in a non-model organism transcriptome
I have several assembled, annotated transcriptomes of non-model organisms (fish). I would like to identify what transposons are present in these transcriptomes (LTR, SINEs, LINEs etc) and compare them....
View ArticleNeed a help re Blastn against short (~50 nt seq)
Hi Evevryone,In stand-alone blast, I'm blasting several thousands of ~450nt long sequences against one short ~50nt long motif sequence to find the sequences that has this ~50nt motif. In blastn output...
View ArticleBlast Illumina Probe Sequence To Get Their Genomic Coordination
Hi all, The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am...
View ArticleHow To Merge Contiguous Blast Hsps! (-M 8 Tab)
Hi, guys! I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap positions...
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...
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