Show Progress (Bar?) For Blast+ Query
Hello everyone,It is possible to visualize the progress of a local blast+ (verbose mode or something [maybe python ou perl])?Thanks in advance!
View ArticleMpiblast Vs Blast+
How up-to-date is mpiBlast compared to blast+ from ncbi? I am not sure what the relation ship between mpiblast and blast+ is, is mpiBlast derived from blast+. blast+ seems to be multi-threaded, but I...
View ArticleCan Biopython Parse Gzipped Xml From Blast?
I have been using blast+ with the xml output format (-m7 in the older days, and outfmt 5 with ncbi-blast+). Since the XML files are huge, I have been gzipping them. I have also been using Biopython to...
View ArticleBatch Blast Two Sequences And Output Sequence Alignment
Dear all,I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.FILE1>gene1_species1...
View Articlerps blast database 'formatrpsdb' problem
Hi.. After installing BLAST+ package from ncbi, when i try to build a database for rps blast analysis using: formatrpsdb -t COG_first -i Cog.pn -o T -f 11 -n COG -S 100.0 it gives following error:...
View ArticleCommand to get BlastDB(Blast Database) information
Hi guys, I have a very simple question on how to get the information on the size of BLASTDB created using standalone BLAST. I have created several BLAST databases and now I need information on their...
View Articleeach protein with each protein
Dear colleagues,I have a lot of proteins. What is thesimplest way to compare each oneof them with all the other proteins?Probably I have to make a databaseand use a program like BlastP.But how to make...
View ArticleHow To Use To Use Standalone Blast In Biopython
I've been trying to get Biopython to use BLAST (the standalone version) and it doesn't seem to work. I'm using blast 2.2.28, python 2.6 and biopython 1.61. I was wondering if anyone could give a short...
View ArticleWhat Is A More Meaningful E-Value For 90Bp Pair-End Illumina Data?
Hi all, I used to use e-value <= 1e-5 for getting any meaningful blast alignment results. Just saw this statement in BLAST FAQ"The lower the E-value, or the closer it is to zero, the more...
View ArticleHow Can I Save A Blast Record (.Xml) Into A Suitable Format For Excel (.Xls)?
I have made a BLAST search through the NCBIWWW.qblast command in Biopython. After having my results saved in a .xml format (by result_handle way, following Biopython tutorial chapter 7) I have parsed...
View ArticleRetrieving Complete Cds From Ncbi
Hi,I was trying to retrieve complete cds sequences from NCBI for a certain protein of interest, say acetyl coa transferase. I did an advanced search as below:((("acetyl coa acetyl transferase"[Protein...
View ArticleFASTA-Reader: First data line in seq is about 100% ambiguous nucleotides...
I am not sure if this is a problem or if in fact the process is correct. Any help is much appreciated. I am trying to make blast databases from assembly fasta files, and have seeing the above error. It...
View ArticleVertebrate Subset Nr Database? Build My Own?
I think I have the answer to my own question, but I'm somewhat new to bioinformatics, and I want to make sure my strategy is sound (and that there are no easier solutions to my problem). We need to...
View Articlemulti-species sequence alignment
Hi all,I have a single 5000bp promoter sequence of a human gene, and would like to do a multi-species sequence alignment to look for conservation. I did some search, but I wasn't able to find any...
View ArticleBlastp And Biopython
I have noticed that when I blast my own database in particular some of the sequences get truncated. This is using my local blast algorithm.For example I know that the sequence FYNTSTPQ and FYNTSTRR...
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 create 10GB blast database
Hello.I want to create a database for local blast but fasta file with reads is 9Gb. So i want from this file to create only one database for the blast and not many files. So i put -max_file_sz argument...
View ArticleRecovering Positions Of Identical Matches From Multiple/ Pairwise Sequence...
I would like to do a pairwise/multiple sequence alignment for a gene from two/three species and then record in a separate file the exact positions of perfect identity between the sequences. Is there a...
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
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?
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