BOL: Related items

Chemical Elements of Bioinformatics

Rahul Agarwal — Tue, 03 Sep 2013 16:35:39 -0500

You must be familiar with periodic table and colour pattern, but this time you are going to amaze by new elements table by Eagle genomics. Just check it out and have fun :)

http://elements.eaglegenomics.com/

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

SOWDHAMINI Lab

Sun, 15 Sep 2013 09:19:12 -0500

Genome sequencing projects have enormous potential for benefiting human endeavors. However, just as acquiring a language's vocabulary does not enable one to speak it, databases that list the amino acid composition of proteins do not directly tell us much about these proteins' higher-level structure and function. The most productive way to indirectly exploit these databases has been to start with the small number of proteins that are fully-characterised and to assume that other "similar" proteins will have a related structure and function. Proteins with very similar amino acid sequence are "no-brainers", but the real test, which our group largely focuses on, is to detect the "essential" similarity in proteins whose non-critical sections have experienced random rearrangements during evolution. In such cases functionally similar proteins may have less than 25% sequence overlap.

More @ http://www.ncbs.res.in/sowdhamini/groups_sowdhamini.htm

BLAST+ 5: Key Updates and Enhancements for Modern Bioinformatics

LEGE — Sat, 07 Dec 2024 22:37:48 -0600

The BLAST+ 5 (Basic Local Alignment Search Tool) update has introduced several key enhancements aimed at improving performance, user experience, and compatibility with evolving genomic data standards. Here are the major updates:

Database Enhancements:
- The BLAST databases have shifted fully to the version 5 (v5) format, which integrates built-in taxonomy information. This allows for more detailed and efficient sequence annotation and analysis.
- Protein databases in v5 are now accession-based, supporting a broader range of sequences, including those from high-throughput projects and the Pathogen Detection Project. These databases also accommodate structural proteins with multi-character chain identifiers.
Performance Improvements:
- Adaptive Composition-Based Statistics (CBS) is available as an experimental feature, enhancing the detection of novel results in protein-protein comparisons.
- Updated algorithms improve the stability of search results, especially when fewer hits are requested than the default output.
Compatibility:
- Support for the older v4 databases has been discontinued. The v5 format is now the default for all BLAST database updates, ensuring alignment with current standards in bioinformatics.
User-Friendly Changes:
- Naming conventions for databases have been simplified to enhance clarity and ease of use. For example, database names no longer include version tags like "_v5".
Future-Proofing:
- BLAST+ 5 aligns with current and upcoming data requirements, ensuring that researchers have access to the most comprehensive and modern resources for sequence alignment.

These updates reflect NCBI's commitment to maintaining BLAST as a leading tool for sequence analysis. For detailed release notes and additional guidance, refer to NCBI Insights here

Fastq format

Jit — Wed, 03 May 2017 04:23:32 -0500

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

It was originally developed at the Wellcome Trust Sanger Institute to bundle a FASTA sequence and its quality data, but has recently become the de facto standard for storing the output of high-throughput sequencing instruments such as the Illumina Genome Analyzer.^[1]

Address of the bookmark: https://en.wikipedia.org/wiki/FASTQ_format

maftools

Surabhi Chaudhary — Fri, 17 Dec 2021 03:18:28 -0600

With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Genome Atlas Project has sequenced over 30 different cancers with sample size of each cancer type being over 200. Resulting data consisting of somatic variants are stored in the form of Mutation Annotation Format. This package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner from either TCGA sources or any in-house studies as long as the data is in MAF format.

https://www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html

Address of the bookmark: https://github.com/PoisonAlien/maftools

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Thu, 14 May 2020 15:13:30 -0500

gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/

Address of the bookmark: https://github.com/kammoji/gapFinisher

Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences

Jit — Tue, 26 Apr 2016 12:18:49 -0500

Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For visualisation, Smash outputs a SVG image, with an ideogramoutput architecture, where the patterns are represented with several HSV values (only value varies). The method can perform both in small- and large-scale. Nevertheless is more directed to large-scale since that the main aim of the research is to know where the large-scale [chromosomal by chromosome] of several primates was equal/different, having at a glance a map of the entire genomes.

Address of the bookmark: http://bioinformatics.ua.pt/software/smash/

Spines

Jit — Mon, 28 Nov 2016 05:33:26 -0600

Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments, variation etc.), as well as specialized tool sets for various analyses. It also features three sequence alignment packages: Satsuma, a highly parallelized program for high-sensitivity, genome-wide synteny; Papaya, an all-purpose alignment tool for less diverged sequences; and SLAP, a context-sensitive local aligner for diverged sequences with large gaps.

Access Spines here.

Address of the bookmark: https://www.broadinstitute.org/genome-sequencing-and-analysis/spines

Harvest

Jit — Tue, 31 Jan 2017 10:57:56 -0600

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees.

Tools

Parsnp - Core-genome alignment and analysis
Gingr - Interactive visualization of alignments, trees and variants
HarvestTools - Archiving and postprocessing

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biology, 15 (11), 1-15 [PDF]

Address of the bookmark: http://harvest.readthedocs.io/en/latest/index.html