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Questions tagged [blast]

Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.

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blast command line

I would to use blastx from command line to analize a library produced with RepeatScout in format .fasta to find new transposable elements. I use this command ...
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How is BLAST's nr database created?

Is there a paper or web page describing the procedure for creating the nr database used by NCBI's BLAST implementation? I presume it's some type of clustering, but I'm curious about how exactly ...
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36 views

Alignment for predicting DNA hybridization?

I am currently working on a Computer Science project where we are trying to build a large set of orthogonal single-stranded DNA sequences. The goal would be to ensure that when put in solution, the ...
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How to filter blast results from blast run against virulence factor database

I downloaded virulence factor database from here , to predict virulence genes from few genomes that my lab sequenced. I performed local blast on the database with default setting and found around ...
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Merging / Concatentating BLAST Databases

I was wondering if any one has had success merging BLAST databases from multiple references? For a concrete example I have hg19 and a bunch of viral and bacterial genomes that all have been index ...
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37 views

taxon exclude list for searching local blast database using blastn

I am looking for a solution to exlude certain entries when searching a local blast nt database (with blastn), specifically the sequences from uncultured / environmental samples, ideally using their ...
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How to retrieve the best-scoring Trinity isoform from blastx results

I'm working on a somewhat unusual transcriptome focused on a killer X chromosome. This chromosome has some new genes, with expression levels quite different from their autosomal paralogs. I've found ...
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79 views

Hits in Primer-BLAST not found with programmatic blastn query

Summary: I'm writing an automated tool for designing Sanger sequencing primers (other tools don't do exactly what I want) that will be incorporated in a production diagnostic laboratory for on-demand ...
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Randomness in BLAST

So if you see the BLAST parameters it says The Expected value E is a parameter that describes the number of hits one can "expect" to get by chance when searching a database of particular size. It ...
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How BLOSUM Matrix is constructed and calculated

I would like to ask how BLOSUM matrix is constructed and calculated ? I read the wikipedia and I still do not understand it. I do not understand the mathematical calculations as I have low knowledge ...
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How to get the longest fasta sequence including all possible switching isoforms of a gene out of isoforms

I am working with RNA-seq data without a reference genome/transcriptome and am instead using a Trinity de novo transcriptome assembly. I analyzed both isoform and gene expression abundances using RSEM....
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181 views

Can't install newest Blast from Conda

I have run into an odd situation, where Anaconda repo page clearly states that the newest version of Blast in Bioconda channel is 2.7.1, however the version Conda wants to install (command ...
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Fast and reliable alternatives to blast

After some unexpected results (and previously reported) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate. I only found hmmer, but I don'...
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Finding orthologues using BLAST on the NCBI database

I'm an informatics student who has essentially zero knowledge of biology. I BLASTed my gene and have 1000s of results with very low E values. Where do I go from here if I want to find orthologues?
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API/website for blasting peptide sequence against database of all plant proteomes

I would like to blast a peptide sequence against all available plant proteome databases, i.e. a blastp metaproteome analysis. What tools are available? Which ...
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Does anyone have older versions of NT and 16s RNA DB from NCBI?

I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied: Unfortunately, we do not archive past versions of the blast ...
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228 views

Calculating bit score: How do you find lambda and K?

To calculate bitscore from score you can use this equation: $S' = (lambda*S - ln(K)) / ln(2)$ If I am trying to manually calculate the bitscore of an HSP of a pairwise blastn alignment, and I know ...
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How to achieve blast results according to the intuitive interpretation of `-max_target_seqs`?

Very recently a BLAST parameter -max_target_seqs n got a lot of attention. Instead of the intuitive interpretation (return the best ...
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Downloading full search results from BlastKOALA?

I have just started using BlastKOALA KEGG which has been useful in annotating (aminoacid) sequences. This is their website: https://www.kegg.jp/blastkoala/ When you get results, there are links for ...
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The algorithm behind makeblastdb?

What is the algorithm/concept behind‚makeblastdb? I know makeblastdb produces a .phr, ...
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30 views

Bioinformatics approach to dentifing potential PCR primer sequences for transcribed gene

I have an annotated transcriptome and would like to develop PCR primers for particular transcribed genes. My species is a non-model plant. Can I use BLAST or another tool to identify potential PCR ...
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27 views

Batch detection of CRISP proteins in fasta file

Probably a naive question. I am inexperienced. I am interested in identifying potential CRISP (Cysteine-rich secretory proteins) in a certain tissue transcriptome (ca. 20k sequences in fasta). I ...
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257 views

How to interpret a PSSM matrix from PSI-Blast - what do the numbers represent?

PSI-Blast on a sequence returns a PSSM matrix file containing two matrices, one to the left, one the the right, for all amino acids: ...
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What does an output of -I for all amino acids mean in a psi-blast pssm matrix file?

I have run psi-blast using the NR database, remotely, with one iteration, for several sequences to calculate an evolutionary profile (PSSM) for each of those sequences. However, many of the PSSM ...
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BLAST(n): No hits found

I am currently exploring the BLAST program, just for testing purpose i generated two FASTA files, containing two genes A and B, such that B is just a motif of repeated 'G's that occurs in A. file A....
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Will blastn remove sequences from a search with low identity?

I'm using this command (excuse the duplicate naming, I know it's bad form): ...
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Official documentation for textual BLAST output?

This is pretty vexing: I got asked to explain the meaning of the match line in a blastp output, especially the subtle difference between a blank and plus. E.g.: ...
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66 views

Is it OK to use Blast+ to query NCBI's 16s rRNA database with 16s DNA sequences?

I have 16S DNA sequences from diversity sequencing, and want to query these against NCBI's 16S rRNA database. If I ultimately want to get taxids for the species that my sequences have, does it make a ...
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assigning different characters to present and absent genes from blast output using perl or python

I have file called pangenome.txt which has only one column containing the names of the genes ...
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166 views

Blast hits disappearing after changing -evalue

I was teaching an introduction to bioinformatics when the students and I noticed strange Blast behavior that we couldn't explain. With the default evalue parameter,...
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How to download the whole BLAST nt database into a specific folder?

I have successfully downloaded the whole nt BLAST database into the current folder using: wget -b "ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.??.tar.gz" However, I ...
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Biopython - extracting query coverage from XML Blast output

I need to extract (or to calculate precisely) the query coverage from Blast output. Now I use NCBIWWW.qblast to query Blast in XML format. Is it possible to know the query coverage parsing the XML ...
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Mirbase and blast locally

I am trying to reproduce locally on my computer what I get running mirbase on their website using BLAST. The search sequences is: mature miRNAs which I had downloaded on my computer and make it as a ...
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616 views

Why does a very strong BLAST hit get lost when I change num_alignments, num_descriptions or max_target_seqs parameter?

Disclaimer: This is a self answered question for documentation purpose and I adapted this from the following github gist. Especially from users terrycojones and peterjc as well as sujaikumar who ...
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Error “Can't locate List/MoreUtils.pm in @INC” when I run update_blastdb.pl

I encoutered some technical problem when learning BLAST as below: After I use conda install blast to install ncbi-blast, and run the command: ...
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How can I only get the species name for fasta sequences from blast results?

I am trying to make a phylogenetic tree from sequences obtained with blast. I have files that contains hundreds of fasta protein sequences which are all named like ...
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Using large databases with BLAT

I'm a computer scientist working with biologists at a small school that doesn't have dedicated bioinformatics staff. I apologize if I use incorrect terminology since I have limited bioinformatics ...
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588 views

Why is this makeblastdb command not working?

I am trying to make local databases for the ncbi-blast+ package (version 2.60). I am doing so for 4 T-cell receptor genes. 3 of the 4 (TRAV, TRAJ, TRBV) have worked fine, but I am having problems with ...
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145 views

Transform traditional blast output to `--outfmt 6`

I already run a blastx of many metagenomic databases (raw illumina reads) against the nr database. However, I forgot to add the --outfmt 6 argument to the code and ...
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2answers
57 views

Major variability in speed of BLAST between proteins

I'm running blast+ searches for a list of proteins using specific parameters. This is my search ...
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400 views

creating graph of distribution of blast hits on the query sequence

I'm attempting to visualize the results of my BLAST search in a way similar to the graphical display of the distribution of blast hits from the web BLAST. For example, from my BLAST search: except I ...
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1answer
20 views

blasting a refseq protein does not show the protein in the result set

Can anyone explain me, why I don't find a specific protein with a blast that was took before from the NCBI refseq database? Specifically, I was trying to blast the protein with the accession number "...
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377 views

changing blast parameters using NCBIWWW module

I have found a blog post with a script that I would like to use for my current research project: link The script is incredibly fast and produces a smooth conservation plot. In the blog post, the ...
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319 views

A tool or webserver for building PSSM matrix

I have some protein sequences and I want to build a position-specific scoring matrix (PSSM) for them and then upload this PSSM to NCBI PSI-BLAST. I used CHAPS program for this pupose but uploading the ...
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1answer
346 views

how to set database other than nr for remote blast+ search

I am attempting to run a BLAST search remotely using BLAST+. I can get search to work correctly at the command line with the following commands: ...
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1answer
60 views

Duplicate long hits from PSI-BLAST

I had a protein Refseq ID and I PSI-BLASTed this sequence against Refseq database. We all know that the Refseq is a Reference sequence database and it shouldn't have redundancy. After BLASTing my ...
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3answers
447 views

How does blastn sort output?

I used blastn to search one a genome database for the sequences in a file. ...
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1answer
1k views

How to extract fasta from a blastdb

How to extract the sequence used to create a blast database. This is useful when you download a blastdb from somewhere else e.g. one of the databases provided by NCBI including the 16SMicrobial ...
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3answers
175 views

What command/invocation is used to generate NCBI 16SMicrobial blastdb

I'm looking for the exact invocation used to generate the 16SMicrobial database that you can download from here: https://ftp.ncbi.nlm.nih.gov/blast/db/ I'm hoping to create the same type of blastdb ...
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1answer
109 views

Why do BLASTn and prokka not seem to be searching the whole fasta file?

When I use blastn and prokka (I will detail exactly how I did so below) on a 2.8 million bp fasta file I get output start/end numbers that do not seem to cover the entire genome. Starting with a ....