BOL: Related items

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

Genomic Scientist at UDSC

Thu, 28 May 2015 19:14:23 -0500

Centre for Genetic Manipulation of Crop Plants

Department of Genetics

University of Delhi South Campus

NEW DELHI – 110 021

WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT & LAB / FIELD ATTENDANT

1 Research Scientist (RS) – 3

DBT, Ph. D.

Experience on DNA Markers, plant genome mapping and bioinformatics

Salary: 60,000 (Consolidated) + 5% annual increment

Date and time: 25.06.2015 at 10:30 AM

These temporary positions have been sanctioned in a DBT funded project for the Phase II on ‘Centre of Excellence on genome mapping and molecular breeding of Brassicas.’

The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room.

Applicants are requested to bring all related documents, in original and a set of photocopy, for verification.

No TA/DA will be paid for attending the interview.

www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=5492&cntnt01returnid=83

Genomic Open-source Breeding informatics initiative

BioStar — Wed, 06 Jan 2021 19:42:21 -0600

To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding programs.

To transform breeding by connecting diverse data with precision breeding tools to advance yields and adaptation to local growing conditions, bringing global communities closer to a sustainable, reliable food supply.

Address of the bookmark: http://cbsugobii05.biohpc.cornell.edu/wordpress/

BEDOPS v2.4.26: high-performance genomic feature operations

Jit — Mon, 12 Jun 2017 10:11:01 -0500

BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The overview section of the BEDOPS v2.4.26 documentation summarizes the toolkit, functionality and performance enhancements. The reference table offers documentation for all applications and scripts.

Address of the bookmark: https://github.com/bedops/bedops

kraken: A universal genomic coordinate translator for comparative genomics

Jit — Thu, 07 Dec 2017 04:45:43 -0600

If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomics

Address of the bookmark: https://github.com/nedaz/kraken

HiGlass: a tool for exploring genomic contact matrices and tracks.

Jit — Mon, 11 Jun 2018 09:44:49 -0500

HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (2014) http://higlass.io/

Address of the bookmark: http://higlass.io/

swgis v2.0 : a seqword genomic island sniffer

Abhimanyu Singh — Thu, 01 Nov 2018 12:35:52 -0500

swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in the eugi database.

download swgis v2.0

Address of the bookmark: http://eugi.bi.up.ac.za/eugi_download_swgis.php

Apollo: First instantaneous, collaborative genomic annotation editor available on the Web

Jit — Fri, 31 May 2019 19:55:39 -0500

Apollo is a plug-in for the JBrowse Genome Viewer.
In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’.
History tracking with undo/redo functions is available.
Users are able to directly set an annotation to a specific state, choosing from the ‘History’ display.
Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.
Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.
Users may access a ‘Recent Changes’ page.
Help page with Apollo specific content is available.

Address of the bookmark: http://genomearchitect.github.io/

Phytozome v12.1: plant science community hub for accessing palnts genomic data

Surabhi Chaudhary — Tue, 17 Mar 2020 07:30:17 -0500

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.

Address of the bookmark: https://phytozome.jgi.doe.gov/pz/portal.html