BOL: Related items

Circoletto: visualizing sequence similarity with Circos

Jit — Fri, 09 Feb 2018 10:23:40 -0600

Circoletto, an online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results.

Online version and downloadable software package for offline use (source code in PERL) freely available at http://bat.ina.certh.gr/tools/circoletto/

Contact:ndarz@certh.gr

Address of the bookmark: http://tools.bat.infspire.org/circoletto/

TwinBLAST: When Two Is Better than One

Jit — Sat, 07 Sep 2019 08:50:08 -0500

TwinBLAST is a web-based tool for viewing 2 BLAST reports simultaneouslyside-by-side. It uses ExtJS (www.sencha.com/products/extjs/) to provide 2independently scrollable panels. BioPerl (www.bioperl.org) is used to indexraw BLAST reports and Bio::Graphics is used to draw pictograms of the BLASThits.

https://github.com/IGS/twinblast

https://mra.asm.org/content/8/35/e00842-19

Address of the bookmark: https://github.com/IGS/twinblast

BEAP: Blast Extension and Assembly Program

Shruti Paniwala — Mon, 11 Jun 2018 04:52:56 -0500

The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference. https://www.animalgenome.org/tools/beap/

Address of the bookmark: https://www.animalgenome.org/tools/beap/

OpenCPU

Rahul Nayak — Sun, 05 Jul 2015 18:34:46 -0500

OpenCPU is a system for embedded scientific computing and reproducible research. The OpenCPU server provides a reliable and interoperable HTTP API for data analysis based on R.

The OpenCPU JavaScript client library provides the most seamless integration of R and JavaScript available today.

OpenCPU uses standard R packaging to develop, ship and deploy web applications. Several open source example apps are available from Github.

Installing your own OpenCPU server is super easy and only takes a few minutes.

More at https://www.opencpu.org/

NCBI PSI-BLAST Tutorial

Fri, 23 Aug 2013 02:25:02 -0500

http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.

A fast package to parse BLAST

Jitendra Narayan — Tue, 10 Sep 2013 16:58:56 -0500

In current era, we are handling huge amount of genomics data, and analysing it to make some biological sense out of it. Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. There are several BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations over them.

Massimiliano Orsini and Simone Carcangiu develope a new and fast fast package "BlaSTorage" to parse and store BLAST results. BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.

Find more @ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571973/

http://biowiki.crs4.it/biowiki/MassimilianoOrsini

BLAST Ring Image Generator (BRIG)

Anjana — Fri, 30 Sep 2016 09:18:50 -0500

BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at: http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page: http://sourceforge.net/tracker/?group_id=328245.

Features:

Images show similarity between a central reference sequence and other sequences as concentric rings.
BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

Address of the bookmark: http://brig.sourceforge.net/

Converting BLAST output into CSV

Poonam Mahapatra — Mon, 11 Dec 2017 04:17:58 -0600

Suppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something.

As with most programs that run on UNIX, the text output is in some specific format. If the program is popular enough, there will be one or more parsers written for that format – these are just utilities written to help you retrieve whatever information you are interested in from the output.

Let’s conclude this tutorial by converting the BLAST output in out.txt into a spreadsheet format, using a Python script.

First, we need to get the script. We’ll do that using the ‘git’ program:

git clone https://github.com/ngs-docs/ngs-scripts.git /root/ngs-scripts

We’ll discuss ‘git’ more later; for now, just think of it as a way to get ahold of a particular set of files. In this case, we’ve placed the files in /root/ngs-scripts/, and you’re looking to run the script blast/blast-to-csv.py using Python:

python /root/ngs-scripts/blast/blast-to-csv.py out.txt

This outputs a spread-sheet like list of names and e-values. To save this to a file, do:

python /root/ngs-scripts/blast/blast-to-csv.py out.txt > ~out.csv

If you have Excel installed, try double clicking on it.

BLAST+ 2.11.0 release is now available on FTP site !

Jit — Sat, 14 Nov 2020 21:37:53 -0600

BLAST+ 2.11.0 release is now available from our FTP site. The main advance is the ability to provide usage reports to NCBI to help us improve BLAST. This information is limited to the name of the BLAST program, some basic database metadata, a few BLAST parameters, as well the number and total size of your queries. See the Privacy document for more details on the information we collect, how we will use it, and how you can opt-out of reporting.

Another new feature allows threading by query batch in rpsblast/rpstblastn. Enabling this option using -m t provides more efficient searching with large numbers of queries. See release notes for details on more improvements and bug fixes.

Useful Links
------------
NCBI Insights: https://ncbiinsights.ncbi.nlm.nih.gov/2020/11/12/blast-2-11-0/

BLAST FTP: https://go.usa.gov/x7QQ3
Privacy document: https://go.usa.gov/x7QQe
Release notes: https://go.usa.gov/x7Qnv

Basics of BLAST Programs !

BioStar — Fri, 26 Jul 2024 06:04:26 -0500

The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.