Any Way To Ncbi Blast Multiple Protein Sequences?
Is there any tools or any direction anyone can point me in towards Blasting multiple amino acid sequences on http://blast.ncbi.nlm.nih.gov/Blast.cgi ?I could potentially write a script to do this and...
View ArticleHow To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
I saw that tblastn is capable of doing that kind of search, but I want my position-specific scoring matrix (pssm) to be built from nucleotide, not protein, sequences.Has anyone done something similar...
View ArticleProblems In Creating Pssm Using Psiblast
Hi, Everyone.Recently I am using PSIBlast to create PSSM.Command seems like this: psiblast -subject oneseq.fasta -inmsa alignment.fasta -outascii_pssm pssm.txtThe problems is Error: NCBI C++ Exception:...
View ArticleBlast+ Query Splitting/Chopping In Blastxml Format
What's the easiest way to split a BLAST+ query into pieces BLAST+ all of the chunks with blastn against NT, and merge them back together? I presume using query_loc is better than literally splitting...
View ArticleNcbi Blast Two Parameters'S Question
Hello, I don't know NCBI BLAST two parameters, here they are: -num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Default = `500' -num_alignments...
View ArticleCan You Explain The Differences Among These Blast Databases?
I am trying to blast my sequence against primate databases remotely. But there are so many databases, and most are in abbreviation. Can you explain what they are in the below example list? chimp AACZ...
View ArticleConvert Blast Output Into Blast-Xml
Hey!Problem: I need to convert a standard Blast report into the blastxml format.Background: For speed reasons, I am using UBlast (Usearch) instead of NCBI-Blast. UBlast outputs either tab-delimited...
View ArticleSequence Blast Against Rfam Database
Hi All,I am using blastn to blast my data against tRNAs which is extracted from RFam database. Then I picked one match from the blast result to confirm it by directly searching my read in RFam online...
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 ArticleHow To Perform A Blast Search From A Java Application?
Hello everyone,I would like to perform a Blast Search form within a Java application, i.e. I want to submit the query and evaluate the results. I have stumbled upon several jars on the web, but none of...
View ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
View ArticleLimit The Memory Size Of Blast?
Would anyone tell me whether it is possible to limit the memory size in blast+/blastall search? If possible, how should we do it? Thanks!
View ArticleBlast Database Size Influence On Number Of Significant Hits
I have a set of gene sequences and specific sequence.cat genes.fa>Gene_1_chr1_1000_1200 ACGT...>Gene_2_chr2_3000_3400 TTAT... cat sequence.fa >Searchable_sequence ACGG... I want to search for...
View ArticleHow To Get Fasta Source File From Blast Csv Format?
I am currently writing a library that uses the -outfmt 10 option of Blast, which give you a CSV instead of the pretty human readable format.Liketblastn -db dmel_a -query somequery.faa -outfmt 10The...
View ArticleHow To Acquire A Pssm Of A Protein Fasta With Ncbi-Blast-2.2.29+
I am a newcomer to ncbi-blast-2.2.29+. Previously, I had been using blastpgp to gain PSSM. In blastpgp, to gain a PSSM of a protein fasta, I ran command as follows:blastpgp -a $BLAST_NUM_CPUS -t 1 -i...
View ArticleHow To Remove All Sequences In My Custom Blast Database?
Is it possible to clear a blast database once you have made it? I mean I created my custom database with nucleotide sequences, but I think I messed up something so I need to empty/clear my database and...
View ArticleHow To Extract Max Score Blast Hit Among A Huge Data Set?
Hi everyone, I want to extract max score blast sequence among 50 genomic data set : my approach like this:I did all the denovo assembly of all 50 genome.Next i predicted all the ORF using Prodigal: (A...
View ArticleIncomplete Blast Database In Ubuntu
hello all, i am trying to do local blast using this command blastall -p blastn -n T -i query.fasta -d nt.12 -o /blast.outi am doing a "blastn" , "-n T" shows i want to megablast. i have downloaded...
View ArticleAny Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View ArticleHow To Examine Whether Homology Search Method Used(Blast/Hmmer) Is Feasible...
Hallo...how to one examine whether homology method used is feasible for identification of a particular gene family e.g HSP. Suppose i have identified 550 sequences suspected to be a particular gene...
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