Most Sensitive Method To Search 100-1000Bp Sequences To Genome At Human-Mouse...
Following up on this question: http://biostar.stackexchange.com/questions/8010/searching-200-400bp-matches-against-mammalian-genome-human-mouse-distance I would like to know what is the most sensitive...
View ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View ArticleCompute Blastx E-Value
Does anyone know how blastx e-values are computed? Is it the same as blastp, except the query sequence is divided by 3? I've tried using E = (m/3)n2^(-S), but I get slightly different results than from...
View ArticleVisualization of tblastn results
Hello. i am creating a web interface application , that in one step , it runs localy tblastn (a contig against sra database). So the output of the tblastn is something like this : Sequences producing...
View ArticleBlast2Go Graphs
I perform blast in the blast2 go and then the GO and annotation steps. In previous projects I had the option to create "direct Go count" graphs on the process, function and component. I remember that...
View ArticleNcbi Legacy Blast Usage With Tblastn/Pssm
I'm trying to get a webservice for protein discovery running. I would like to perform a tblastn with a PSSM from NCBI's archive (smp file). This works fine with NCBI BLAST+, but unfortunately the...
View ArticleBiopython Ncbixml: Retrieve Used Word_Size
I know I can retrieve the expect value, window_size etc that was used submitting the query from the Blast recordclass, but I don't seem to find the wordsize as well. Is there any way to retrieve the...
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 ArticleBLASTP many pairs of peptide sequences
Dear all,I have many pairs of protein sequences, an example shown below.MDDDIAALVVDNGSGMCKAG DDDIAALVDNSGSMCKAGTTAEREIVRDIKEKLCY TTAEIVRKEKLCYVARMQKEITAPSTMKIKI KEITALPSTMKIKII... ...I need to...
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 ArticleHow Can I Download The Results From An Ncbi Blast Search?
I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download...
View ArticleHow To Run Genome Wide Local Blast
Hi Everyone, I have been given a task to compare one gene sequence among 50 strain of E.coli. For this study i have 50 genome scaffold file and one gene sequence file. Now my work will be compare the...
View ArticleNcbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
View ArticleTrying To Extract Blast Results Into Xml Outfile From Larger Blast Xml File
This is probably a fairly basic question, so I apologize in advance, but I can't seem to figure out how to output xml format using Biopython. Basically, I have a fairly large BLAST results file in xml...
View ArticleRaw Alignment Score Calculation
Thanks for lots of answers and I've started with lots of sources here. It helps me to get a good introduction to blast.After I've now a little more understanding I can ask more specific questions such...
View ArticleAnnotating Sequences For Gbrowse - Which Is The Database And Which Is The Query?
Let's say I have some small sequences that I wish to display in Gbrowse. I want to create tracks from Blast results to show where genic regions might be.Do I create a Blast index of the small sequences...
View ArticleUsing Blast2Go From The Command Line
Hi,I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to...
View ArticleMegaBLAST vs NUCmer
Hi,For a project I'm trying to find out which aligner is best for aligning whole bacterial genomes.Important aspects for choosing the best aligner are speed and sensitivity. In this situation NUCmer...
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 ArticleLocal Blast: Querying A Single Sequence Without Input File. Possible ?
Hi,When using BLASTALL by command line, is there any way of querying BLASTALL without using any input file but a directly a sequence ?I would like to do something like:blastall -n blastn -d MyBud.fna...
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