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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 Promotor -35 to -10

I am trying to probe the genome database library across a genus Clostridium for a promotor sequence using just the -35 to -10 region using "N" to denote a 17bp gap. The species where the sequence ...
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15 views

BLAST Promoter -35 to -10

I am trying to probe the genome database library across a genus Clostridium for a promoter sequence using just the -35 to -10 region using "N" to denote a 17bp gap. The species where the sequence ...
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1answer
31 views

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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4answers
45 views

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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1answer
33 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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2answers
69 views

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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1answer
38 views

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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49 views

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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19 views

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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1answer
57 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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99 views

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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0answers
50 views

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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1answer
54 views

The algorithm behind makeblastdb?

What is the algorithm/concept behind‚makeblastdb? I know makeblastdb produces a .phr, ...
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1answer
26 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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1answer
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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1answer
89 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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1answer
79 views

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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1answer
136 views

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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34 views

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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2answers
46 views

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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44 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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3answers
62 views

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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1answer
132 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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1answer
968 views

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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145 views

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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91 views

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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437 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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327 views

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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113 views

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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1answer
84 views

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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1answer
417 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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2answers
126 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
53 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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1answer
301 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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288 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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3answers
254 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
251 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
54 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
259 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
612 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
150 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
94 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 ....
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1answer
66 views

What is the difference between SAM mapping quality and Blast E-value?

Blast reports E-values, but short-read mappers report mapping qualities. Are they the same thing? Can they be converted to each other? If not, why blast doesn't report mapping quality while short-read ...
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2answers
209 views

Understanding the significance of BLAT score calculations for read fragment alignment

I'm attempting to reconstruct the read fragments that form a hit to a target, excluding/skipping gaps. BLAST's outfmt 6, and alternatives such as Diamond's ...