BOL: Related items

Biological databases !

BioStar — Wed, 12 Feb 2020 01:16:29 -0600

Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

Coronavirus Resources !

Neel — Wed, 25 Mar 2020 17:11:33 -0500

2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.

Annotation

https://bigd.big.ac.cn/ncov/variation/annotation

Genome wharehouse

https://bigd.big.ac.cn/gwh/browse/index

Released Genome

https://bigd.big.ac.cn/ncov/release_genome

Download data

ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/

Raw data

https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae

Address of the bookmark: https://bigd.big.ac.cn/ncov/about

YASS :: genomic similarity search tool

Jit — Mon, 02 May 2016 09:26:00 -0500

YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step (as provided for example by iedera).

Main features of YASS are:

multiple, possibly overlapping seeds and a new hit criterion to ensure a good sensitivity/selectivity trade-off
transition-constrained spaced seeds to improve sensitivity (transition mutations are purine to purine [A<->G] or pyrimidine to pyrimidine [C<->T])
using different scoring schemes with bit-score and E-value evaluated according to the sequence background frequencies
parameterizable output filter for low complexity repeats
reporting of various alignment statistical parameters (mutation bias along triplets, transition/transversion)
post-processing step to group gapped alignments

Address of the bookmark: http://bioinfo.lifl.fr/yass/

Mauve: a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion

Jit — Sat, 24 Dec 2016 09:20:53 -0600

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Address of the bookmark: http://darlinglab.org/mauve/mauve.html

Laj: viewing and manipulating the output from pairwise alignment programs

Abhimanyu Singh — Wed, 01 Mar 2017 08:35:40 -0600

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.

The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for "Local Alignments with Java". Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

Address of the bookmark: http://www.bx.psu.edu/~ratan/

Mapping NGS

Abhimanyu Singh — Tue, 02 May 2017 07:58:07 -0500

NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...
To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases the full genome sequence but sometimes, a library of EST sequences is used.
In either way, aligning your sequence reads to the reference sequence is called mapping.

The most used mappers of DNA-seq data are BWA and Bowtie for DNA-Seq data and Tophat, STAR or HISAT for RNA-Seq data. Mappers differ in which options they can take in, how fast and how accurate they are. Bowtie is faster than BWA, but looses some sensitivity (does not map an equal amount of reads to the correct position in the genome).

Address of the bookmark: http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data

maf2synteny

Abhimanyu Singh — Thu, 18 May 2017 05:31:30 -0500

A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat)

This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]

Address of the bookmark: https://github.com/fenderglass/maf2synteny

FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

Jit — Fri, 08 Dec 2017 14:41:08 -0600

Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a greedy way taking the symbols from the given pair of sequences (protein or nucleotide) and results in an optimal alignment faster than conventional dymanic programming techniques. It is also better than the heuristic methods with respect to alignment quality.

Address of the bookmark: http://www.isical.ac.in/~bioinfo_miu/FOGSAA.htm

MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (v4) to detect variants.

Rahul Nayak — Wed, 27 Apr 2022 04:34:12 -0500

MUM&Co is able to detect:
Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)
Inversions (>=1kb) and translocations (>=10kb)

Address of the bookmark: https://github.com/SAMtoBAM/MUMandCo

Harvest: a suite of core-genome alignment and visualization tools

Jit — Fri, 08 Dec 2017 07:16:03 -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

Address of the bookmark: https://harvest.readthedocs.io/en/latest/