Blastp Against Human Proteome
Hey guys,I have a list of gi's for about 10000 protein sequences all from vertebrate species. I want to blast these sequences against non-redundant protein sequences only from humans. I will run the...
View ArticleBlast 2.25+ Segmentation Fault When -Outfmt Set To 6,7 Or 10
Hi all!I am running blast 2.25+ and willing to get output in format 7, setting -outfmt 7. However, with this setting I always get Segmentation fault. Same happens with -outfmt 6 and 10. Other settings...
View ArticleBlast_Formatter: How To Choose Which Database To Read From?
Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command:BLAST Database error:...
View ArticlePreview temporary outputfile blast
Hi, Is there a way to peek at blast temporary file? I would like to know what sequence is analyzed in order to foresee how long the program will take to finish. top command shows that it uses around 4...
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 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 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 ArticleGet Pairwise Sequence Identity
Hey,for some project I need to run pairwise sequence alignments (local ones, i.e. Smith-Waterman) on protein sequences in order to produce a similarity matrix based on the percentage of identical...
View ArticleFind Mismatch And Gap Positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleAssessing Quality And Accuracy Of De Novo Genome Assembly
All, I am curious whether anyone out there has a method for assessing the quality and accuracy of de novo genome assemblies? I am currently doing in silico simulations of de novo genome assembly from a...
View ArticleHow do I blast against a specific portion of the nr database?
I would like to blast my sequences against the swissprot database, using local blast. For the purpose of downstream applications, I would like to do this using the copy of the swissprot database from...
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 ArticlePython Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleBlast Search Implementation In Biojava
Hello!I would like to write the BLAST Search algorithm using BioJava for a school project.I can not find any sources, tutorials, nothing in the BioJava Cookbook. I would like to specify the query and...
View ArticleWhy am I getting the BLAST option error: file does not match input format type
COMMAND USED: makeblastdb -in sorted_alu_seq.fasta -dbtype 'nucl' -out aluBLAST option error: sorted_alu_seq.fasta does not match input format type, default input type is...
View ArticleRun A Blast Daemon
I want to run my own BLAST daemon to avoid loading my blast db into RAM for every query.When I google it: I get a page from IBM that is out-of-date and a lot of other pages about Buffy the Vampire...
View ArticleBlast2Go Memory Allocation
I'm running BLAST2GO on a Linux (Ubuntu 10.04 32 bit) machine with 24 GB RAM (8 processors). No matter what I specify for the maximum memory, it only allocates 455 MB RAM, which is not enough for the...
View Articleparsing too large blast result with bioperl OR other methods?
Hi all, Recently I am dealing with bunch of genes to design the appropriate primers. However, it is still hard for me to obtain the homology information of the primers. For example, I need to design a...
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 ArticleWhat'S Faster? "Blastall -P Blastp" Or "Blastp?"
I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of...
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