Make A Custom Blast Library Using The Output Of Another Blast Result
Hi Biostar,I am working on a microbial gene annotation project and I am interested in taking a large number of sequences (say 20,000) and blasting them against the NR database. However, even with a...
View ArticleError in run blastpgp
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
View ArticleDistribution of e-values in Best Reciprocal Blast Hits for Ortholog Mining
Does anyone have an idea of how the distribution of expect values will look when using reciprocal blast to detect orthologs?
View ArticleBLASTP many pairs of peptide sequences
Dear all,I have many pairs of protein sequences, an example shown below.MDDDIAALVVDNGSGMCKAGÂ DDDIAALVDNSGSMCKAGTTAEREIVRDIKEKLCYÂ TTAEIVRKEKLCYVARMQKEITAPSTMKIKIÂ KEITALPSTMKIKII... ...I need to...
View ArticleOnline Tools To "Prettify" Blast Output
Can anyone suggest an online tool, for a non-bioinformatician (not for me you understand, oh no not me), that will make BLAST output "pretty", i.e. add shading to make mismatches and so on more...
View ArticleBlastn / Tblastn : Mapping The Features Of The Query To The Hit.
I'm blasting+ (blastn+ or tblastn) an annotated sequence (a Genbank.xml sequence (nucleotide or protein) or an Uniprot.xml entry) against a DNA database.Is there a standard tool to map the features of...
View ArticleScientific Names In Blast Output And Databases
Hi, I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option -outfmt which can take sscinames(seems new in version Blast+ 2.2.28), but even...
View Articleblastn -no_greedy switch
Does setting the -no_greedy switch make blastn behave like Smith-Waterman? The documentation states that the switch allows blast to "use non-greedy dynamic programming extension". It isn't clear to me...
View ArticleHow I Can Find The Sequence For The Gene That I Want To Synthesize?
Hi,I'm starting with bioinformatic, and i want ask u this question:I have this sequence: vpnvrgmgar davylmekrg ikvritgrgr vieqslapgd kikngmqcsl rlg from "penicillin-binding protein dimerization domain...
View ArticleStrange Behaviour Of Bioperl'S Bio::Searchio When Parsing Xml Blast Output
Hello, I've noticed some strange behaviour when parsing BLAST .xml output files (-oufmt 5) using BioPerl's Bio::SearchIO library. I have a simple parser script that looks something like:...
View ArticleRunning Blast For A List Of Pairs
Hi,I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?I tried bl2seq but unfortunately it does not produce the alignment of the whole...
View ArticleObtaining the top matches from blast
Hi,I have downloaded the current version of the stand-alone-blast (ncbi-blast-2.2.29+) and I am trying to use blast (blastn) to find similarity of of a group of nucleotide sequences that I have....
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 ArticleBlastdbcheck Error
I keep getting errors on the following command:blastdbcheck -db nt.00Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing...
View ArticleHow To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.But how to create it? There is a makemat...
View Articlede novo RNA-seq and different assembly options
Hi all -- I'm new to RNA-seq and have had some issues assembling the reads. I'm looking for any advice or input on what might be the best way to handle my data. My work is done in oocytes of a...
View Articleblast output for FASTA (aligned sequences) to get organism name
Hi,I want to get the organism name from blast output (FASTA (aligned sequences)) for the specific protein.I am a beginner in python. Please help me to write the script for getting organism name in...
View ArticleLooking For Frequency Of A Very Specific Rna Editing Event In Publicly...
I am working on a ubiquitously and well expressed gene whose ~1.5 kb-sized transcripts get mutated at one and only one site. The mutation is a nonsense one that changes an ORF codon of the mRNA to a...
View ArticleExact Matching With Bowtie, Blat And Blast+
I am running bowtie with the following parameters, to look for up to, say, 10 exact matches of a 36-base nucleotide string to a GRCh37/hg19 index, _e.g._: $ bowtie -S hg19 -v 0 -k 10 -f sequence.fa...
View ArticleDisagreement When Computing Contig Alignments With Different Tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
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