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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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1answer
24 views

blast nt vs Genbank

What is the difference between these two databases? ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and ftp://ftp.ncbi.nih.gov/genbank/ I understand that BLAST database has both nt for nucleotide and np for ...
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1answer
50 views

Plotting distance tree from blastn output

I'm trying to plot a simple distance tree of my blastn output with nj (like the tree view on NCBI). From what I understood, what I think I should do is extract all the hsps from each alignment re-...
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1answer
66 views

Appropriate tool or algorithm for sloppy alignment of degenerate bases

I have an optimization problem where I have a degenerate nucleotide sequence I want to align against subsets of a reference genome (exons, specifically, to make the problem more tractable). The ...
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1answer
30 views

Huge variability in blastn speed between same short sequence job

I have been running a couple of blast searches and I am very suprised and somewhat frustrated by the huge variability in job completion time. The specifics of my blast search are as follows: Running ...
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29 views

BLAST server download

I discovered that Phytozome's BLAST results look quite nice (please see below). By any chance, does anyone know where to download this BLAST server in order to install it locally for organisms which ...
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22 views

Retrieve sequence data from just one geneID and not the identical sequences with blastdbcmd

I'm trying to retrieve the sequence from the gene id in NCBI's nr. If I try doing blastdbcmd -db nr -entry 1008808716 I get with this result: ...
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1answer
38 views

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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2answers
143 views

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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1answer
51 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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1answer
56 views

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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1answer
36 views

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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1answer
95 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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0answers
20 views

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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1answer
86 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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3answers
97 views

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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3answers
312 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
136 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
378 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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5answers
215 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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2answers
62 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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1answer
59 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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0answers
25 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
405 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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2answers
124 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
78 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
138 views

The algorithm behind makeblastdb?

What is the algorithm/concept behind‚makeblastdb? I know makeblastdb produces a .phr, ...
3
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1answer
32 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
28 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
446 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
91 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
602 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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1answer
41 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
50 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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1answer
79 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
74 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
193 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
3k 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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0answers
269 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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0answers
122 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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1answer
835 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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0answers
722 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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3answers
239 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
102 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
797 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
158 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
61 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 ...
5
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1answer
540 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 ...
4
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1answer
21 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 "...
4
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0answers
460 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
388 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 ...