How Do You Extract The Query Title From A Blast Xml Output Using Biopython
I would like to find the alignment title along with the query title and the expect value in a BLAST XML output file with many query sequences. I can get the alignment title and expect value but the...
View ArticleHow To Filter A Blast Xml Output ?
Hello list, I have very large xml blast outputs (in order to use with blast2go) and I need to reduce these consequently according to a selected criterium (for instance the E-value). Did anybody write a...
View ArticleBlast Parameters For Searching Rna Database
I've a collection of cDNAs (median length ~1500 ) and I wish to filter out those are RNA coding ones thru a blastn search. Can people tell me what typical blast parameters are to be chosen for that...
View ArticleWhy Is Makeprofiledb Throwing Confusing Defline Errors?
I have an alignment file [alignment.aln]:>lcl|21974 MRLQLILTITLLLTSFMGYRDAAVIQGKTERSAMKMRKLLQILHKNSCGCNDDDSDGDDCCFGTCLDNACWPVKKRSSAII can make a blastdb with this file:makeblastdb -in alignment.aln...
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 ArticleBlastx Against Swissprot
HiI want to blastx a huge sequnce set against swissprot (as it takes too long aginst nr), is it possible in a resonable time with a regular hardware and how to install and run it locally?Thanks alot!
View ArticleHow To Get Number Of Hit For A Query??
hi , i'm using biopython to parse my blast xml output i make condition print on the number of for query. i print my query and sbject if the query have only one hit. but it's not working here is my...
View Article(Determine If Necessary And) How To Realign Blast Results For Arlequin?
I am newbie in bioinformatics, and now trying to learn about alignments, so sorry about the lack of vocabulary. After blasting a sequence, this is my output from a BLASTN... lots of other aligns ......
View ArticleHelp In Configuring A Local Blast Server.
Hi all.I am attempting to configure a local BLAST server on a Windows XP machine. I found the following series of explanations helpful but incomplete:http://www.ncbi.nlm.nih.gov/books/NBK52637/Relevant...
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 ArticleBlast Help On Nucleotide Collection Nr/Nt
I am running a local blast server. I can format and blast my own databases. However, I am unsure of how to setup the "Nucleotide collection nr/nt" database from this NCBI Blast URL. Can I just download...
View ArticleParsin Nsq Database For Blast
Hello, I am trying to use biopython to run the local blast. I created the database for Ecoli strain MG6155 and the output results were in nsq format. Now I want to run the local blast using biopython....
View ArticleUsing Blast From Within Perl.
Hi all.I recently installed the latest version of Blast (standalone) on a Win XP machine and altered the appropriate path settings, i.e., C:\blast\bin. Having searched the web for an example of using...
View ArticlePairwise Gene Sequence Similarity Of All Human Genes
As stated, I want to get a matrix which contains pairwise gene-gene sequence similarity of the human genome genes. Are there any databases which contain this table?
View ArticleForum: Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver
Executive Summary: SequenceServer lets you rapidly set up a custom BLAST+ server with an intuitive user interface for use locally or over the web.Why we created it: We were frustrated with:too many...
View ArticleMakeblastdb Hash_Index: What For? When To Use?
The makeblastdb program that comes with blast distribution has the hash_index option that states:-hash_index Create index of sequence hash values.What is for? When should I use it?
View ArticlePerforming Blast/Smithwaterman Searches Directly From My Application
Bringing in my questions from stackoverflow:I'm working on a small application and thinking about integrating BLAST or other local alignment searches into my application. My searching has only brought...
View ArticleHow Can I Get Older Versions Of Psi-Blast Program?
Hi,Do you know how I can get older versions of PSI-BLAST.Right now, I've downloaded 2.2.26, but I need to use these parameters. (Pardon me for the irrelevants). blastpgp -i seq-file -Q...
View ArticleRetrieving Protein Structures
I want to make structural analysis of lysosomal proteins found in mammals. To make start, I would like to retrieve as many structures as possible from the biological database (PDB). These structures...
View ArticleCan Ncbi Blast Only Search A Special Region In Database For Hits?
I want to blast my 36SE reads to a special region of HG19, does NCBI BLAST can do this special region search? If so, how can I do this?for example, I only want my reads to be blasted to chr1:5000-10000...
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