BOL: Related items

gVolante: Completeness Assessment of Genome/Transcriptome Sequences

Jit — Tue, 06 Aug 2019 21:37:56 -0500

gVolante provides an online interface for completeness assessment of user’s original or publicly available sequence datasets as well as for browsing results of completeness assessment performed on publicly available genome and transcriptome assemblies.

Address of the bookmark: https://gvolante.riken.jp/

Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation

Jit — Tue, 16 Mar 2021 05:45:44 -0500

We demonstrate a novel approach forlocal alignment of DNA reads with respect to reference genome.For this process we have used Skip-gram model for creatingencoding(Nucl2Vec) and k-nearest neighbor for the alignment.With our new approach we have reduced computation cost forlocal alignment , while achieving accuracy comparable to existingdefacto standard BWA-MEM tool.

https://prakharg24.github.io/papers/401851.full.pdf

Address of the bookmark: https://prakharg24.github.io/papers/401851.full.pdf

KAST: Perform Alignment-free k-tuple frequency comparisons from sequences

Jit — Thu, 20 Sep 2018 08:56:35 -0500

Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

Address of the bookmark: https://github.com/martinjvickers/KAST

DECIPHER; a software toolset for deciphering and managing biological sequences efficiently using the R

BioStar — Sun, 09 Dec 2018 19:06:17 -0600

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. The R package is distributed as platform independent source code under the GPL version 3 license. Some functionality of the program is accessible online through web tools.

Address of the bookmark: http://www2.decipher.codes/

Gepard: allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes

Jit — Mon, 26 Aug 2019 11:38:30 -0500

Gepard (German: "cheetah", Backronym for "GEnome PAir - Rapid Dotter") allows the calculation of dotplots even for large sequences like chromosomes or bacterial genomes. Reference: Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007; 23(8): 1026-8. PMID: 17309896

http://cube.univie.ac.at/gepard

Address of the bookmark: https://github.com/univieCUBE/gepard

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

Common methods to discover tandem repeats

BioStar — Thu, 09 Mar 2023 02:40:52 -0600

Tandem repeats are DNA sequences that are repeated in a contiguous manner in the genome. These sequences are often used as genetic markers and are important in many areas of genetics and genomics research. Here are some methods for discovering tandem repeats in genomes:

Tandem Repeat Finder: Tandem Repeat Finder is a software tool that identifies tandem repeats in DNA sequences. It is available for free download and can be used on both nucleotide and protein sequences. The tool uses a statistical algorithm to identify repeats based on their length, copy number, and overall composition.
RepeatMasker: RepeatMasker is another software tool that can identify tandem repeats in DNA sequences. It works by comparing the input sequence to a database of known repeats and then identifies any tandem repeats that match those in the database.
PCR-based methods: Polymerase chain reaction (PCR) can be used to amplify and detect tandem repeats in genomic DNA. PCR primers are designed to flank the tandem repeat region, and amplification of the target DNA fragment can be visualized on a gel. This method can be useful for detecting novel tandem repeats and for genotyping.
Southern blotting: Southern blotting is a classic method for detecting DNA fragments in a sample. It can be used to detect tandem repeats by digesting genomic DNA with a restriction enzyme, separating the fragments by gel electrophoresis, and then probing the blot with a tandem repeat-specific probe.

Overall, a combination of these methods can be used to comprehensively identify tandem repeats in genomes.

SVbyEye: R Package to visualize alignments between two or multiple DNA sequences

LEGE — Tue, 17 Sep 2024 02:34:57 -0500

R Package to visualize alignments between two or multiple DNA sequences including
a number of functionalities to facilitate processing of alignments in PAF format.

SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process alignments in PAF format. The tool facilitates the characterization of complex SVs in the context of sequence homology helping resolve the mechanisms underlying their formation. Availability and implementation SVbyEye is available at https://github.com/daewoooo/SVbyEye.

Author: David Porubsky

Address of the bookmark: https://github.com/daewoooo/SVbyEye

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)

Sun, 20 Dec 2015 06:03:43 -0600

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)
Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Mathematics / Applied Mathematics, Stati, Zoology)
Location : Kolkata
Last Date : 31 Dec 2015
Hiring Process : Written-test

NO: 340/ESTB/ADMN/NIBMG/2015-16
Doctoral Research In Biomedical Genomics, Including Statistical Genomics conduct National Institute of Biomedical Genomics (NIBMG)
Information For Students Interested To Pursue Doctoral Research In Biomedical Genomics, Including Statistical Genomics, At The National Institute Of Biomedical Genomics (Nibmg), Kalyan
Eligibility conditions for specific areas of research are :
Statistical Genomics : An applicant who wishes to pursue research in Statistical Genomics should hold a Master's degree (First class or equivalent) in a relevant discipline (Statistics, Mathematics, Bioinformatics, or a related discipline)
Biomedical Genomics : An applicant who wishes to pursue research in any area of biomedical genomics, other than statistical genomics, should hold a Master's degree (First class or equivalent) in a relevant discipline (Biochemistry, Biotechnology, Molecular Biology, Genetics, Zoology, Physiology, or a related discipline)
Fellowship : An applicant should have passed the NET conducted by CSIR/UGC/ICMR/DBT within the past ONE year AND should have been awarded a valid Junior Research Fellowship from CSIR, UGC, ICMR, DBT (Category-I only), DST (INSPIRE), NBHM. Preference will be given to candidates with demonstrable research training in the form of summer training or short-term courses in established research laboratories in preparation for a research career in biomedical sciences
How to apply
Online application will be accepted until 5 PM of December 31, 2015. A formal interview of the short-listed candidates will be held on January 12, 2016

More at http://www.nibmg.ac.in/?q=Career%20Opportunities

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder