Pairwise vs. Multiple Sequence Alignments: Which has better accuracy?
I am aligning many similar sequences from a BLAST result and looking for mutations at certain positions. My inclination is that an MSA (Clustal Omega) is the best approach but my PI is worried about...
View ArticleBlast+ Stand Alone Version For Sequence Alignment
HiOn the on line version of Blastp (link text) there is a sequence alignment section (and it produces E-values for the alignment).and now I want to use the standalone version to perform alignment(My...
View ArticleStandalone Blast Issue
Dear all,I have recently installed blast-2.2.26 on my machine (running MacOS 10.7.3) and I tried to perform a BLAST search using a single protein sequence as query and a formatted (by me) database...
View ArticleHow To Get Ungapped Sequences From Blast Output?
I am interested in getting ungapped sequence hits (hspsnogap) from blast output, I tried using this:result_handle = NCBIWWW.qblast("blastp", "nr", record.format("fasta"),expect=10,"hsps_no_gap")...
View ArticleHow to understand which DNA strand is (5' to 3' ot 3' to 5') in the result of...
Hi!if a have such a result from a blast run, how can i understand if its in the 5' or 3' side of the DNA or protein strand ?> gnl|SRA|SRR456295.4505.2 FIHSSUW02H237H.2 length=250 Length=250 Score =...
View ArticleWhat does sframe signify in BLAST output?
Hi,I am relatively new to the field of Bioinformatics and have just been introduced to BLAST. I'm trying to understand the output available from the BLAST program. As listed in the NCBI manual, I am...
View ArticleBLAST database files
After I run makeblastdb against a fasta file, I get nhr, nin, nog, nsd, nsi and nsq files.Questions1) What do these file extensions mean?2) Do these files replace the original chrY.fa file which was...
View ArticlePython/Perl Script For Defining Minimum Coverage Of Blast Match
Hi - does anyone know of a script that allows for a blast result to be filtered by the minimum total coverage of the query/subject that the alignment/s represent?I'm imagining a script that calculates...
View Articlerecruitment plot - blast output
Hello Guys,Does anyone have a tutorial for generating recruitment plot from a file output blast? thanks!
View ArticleHow I Can Find The Sequence For The Gene That I Want To Synthesize?
Hi,I'm starting with bioinformatic, and i want ask u this question:I have this sequence: vpnvrgmgar davylmekrg ikvritgrgr vieqslapgd kikngmqcsl rlg from "penicillin-binding protein dimerization domain...
View ArticleBlast Short Sequences Containing Repeats
I try to detect repeats using blastn. I use the same sequence as query and subject. The sequence contains a 21bp tandem duplication. I expect three hits: The whole sequence aligns itself.First...
View ArticleHow To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.But how to create it? There is a makemat...
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Tool: Automatically download NCBI Blast databases
HiI thought to share this tool, in case you need it. The tool automatically downloads ALL NCBI blast databases from NCBI ftp server. Limitations:You can stop a download and resume later as long as you...
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 ArticleBest Way To Grab All Ncbi Protein Sequences For A Specific Taxonomic Query?
I would like to retrieve all of the NCBI protein sequences that belong to a specific taxonomic query, or children of that query. For example, I want to get every protein sequence belonging to the...
View Article/Home/Abc/Ncbi-Blast-2.2.25+/Bin/Blastn: No Such File Or....
Hello, I want to set a local blast in my system..but it showing some error while i am working. I have set Environment var path /home/abc/ncbi-blast-2.2.25+/bin in .bashrc file. i also have set the...
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 ArticleError Using Makeblastdb
Hi there,I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta...
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 ArticleForum: How To Correctly Speed Up Blast Using Num_Threads
Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it...
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