BOL: Related items

destruct

Jitendra Prajapati — Mon, 29 Feb 2016 17:34:59 -0600

Destruct is a tool for joint prediction of rearrangement breakpoints from single or multiple tumour samples.

More at https://bitbucket.org/dranew/destruct

Address of the bookmark: https://bitbucket.org/dranew/destruct

QuorUM: An Error Corrector for Illumina Reads

Jit — Wed, 08 Nov 2017 11:40:41 -0600

Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read at every base in the genome. These errors make handling the data more complicated because they result in a large number of low-count erroneous k-mers in the reads. However, there is enough information in the reads to correct most of the sequencing errors, thus making subsequent use of the data (e.g. for mapping or assembly) easier. Here we use the term “error correction” to denote the reduction in errors due to both changes in individual bases and trimming of unusable sequence. We developed an error correction software called QuorUM. QuorUM is mainly aimed at error correcting Illumina reads for subsequent assembly. It is designed around the novel idea of minimizing the number of distinct erroneous k-mers in the output reads and preserving the most true k-mers, and we introduce a composite statistic π that measures how successful we are at achieving this dual goal. We evaluate the performance of QuorUM by correcting actual Illumina reads from genomes for which a reference assembly is available.

QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at http://www.genome.umd.edu.

Address of the bookmark: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821

Pattern Searching in a Single Genome

Aasha — Mon, 07 Mar 2016 05:02:51 -0600

Pattern searching holds much importance for biologists , for the understanding of DNA ( and its functionality) can be more than a matter of satisfying curiosity , but also give answers to many issuess uchas medical conditions . However,there are a number of ways of searching with in a single chromosome.

Address of the bookmark: https://www.stats.ox.ac.uk/__data/assets/pdf_file/0018/5373/LintonFinalReport.pdf

BEAR: Better Emulation for Artificial Reads

BioStar — Sat, 06 Jul 2024 04:27:53 -0500

Created by Stephen Johnson, Brett Trost, Dr. Jeffrey R. Long, Dr. Anthony Kusalik University of Saskatchewan, Department of Computer Science

BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads with read lengths, quality scores, error profiles, and species abundances derived from real user-supplied WGS data.

Address of the bookmark: https://github.com/sej917/BEAR

NovelSeq: Novel Sequence Insertion Detection

Neel — Fri, 09 Jun 2017 04:31:30 -0500

The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

http://novelseq.sourceforge.net/Home

Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

Address of the bookmark: http://novelseq.sourceforge.net/Home

Program Officer, Bioinformatics at Jhpiego

Tue, 29 Aug 2023 00:05:30 -0500

Jhpiego is a non-profit global health leader and Johns Hopkins University affiliate that is saving lives, improving health, and transforming futures. We partner with governments, health experts, and local communities to build the skills and systems that guarantee a healthier future for women and families. Jhpiego translates the best science and practices into moments of care that can mean the difference between life and death for women and families. The moment a woman gives birth; the moment a midwife helps a newborn to breathe. Through our partnerships, we are revolutionizing health care for the world’s most disadvantaged and vulnerable people. In India, Jhpiego works across various states in close collaboration with national and state governments, providing technical assistance in the areas of family planning, maternal and child health, strengthening human resources for health, and non-communicable diseases. These programs are funded by USAID, the Bill & Melinda Gates Foundation, the David & Lucile Packard Foundation, the Children’s Investment Fund Foundation (CIFF), , and other anonymous donors.

The Program Officer, Bioinformatics, operating under the Senior Advisor for Metagenomics & Lab Systems, will play a pivotal role in leveraging bioinformatics to advance the objectives of the Health Security and AMR program. This position offers a unique opportunity to contribute to cutting-edge genomics research and its application in public health.

More detail at https://jobs-jhpiego.icims.com/jobs/5440/program-officer-%e2%80%93-bio-informatics/job

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/

Tools for Sequence translation !

Abhi — Tue, 08 Nov 2022 03:37:58 -0600

BOrf - https://github.com/betsig/borf

CodAn - https://github.com/pedronachtigall/CodAn

EMBOSS-Sixpack - https://www.ebi.ac.uk/Tools/st/emboss_sixpack/

esl-translate - http://hmmer.org/, https://github.com/EddyRivasLab/easel

GeneMarkS-T - http://exon.gatech.edu/GeneMark/license_download.cgi

ORFfinder - https://www.ncbi.nlm.nih.gov/orffinder/ (web server)

PLASS - https://github.com/soedinglab/plass

Prodigal - https://github.com/hyattpd/Prodigal

TransDecoder - https://github.com/TransDecoder/TransDecoder

Research Fellow Bioinformatics

Mon, 04 Apr 2016 05:41:21 -0500

Research Fellow Bioinformatics
Eligibility : BSc(Bio-Tech), MSc(Bio-Tech)
Location : Ludhiana
Last Date : 19 Apr 2016
Hiring Process : Walk - In
Punjab Agricultural University

Research Fellow Bioinformatics job opportunities in Punjab Agricultural University
Qualification : B.Sc. with minimum OCPA 5.00/10.00 basis or 50% marks. ii. M.Sc. in Biotechnology/ Molecular Biology/Molecular Genetics/Bioinformatics/Genetics/Plant Breeding/Plant Breeding & Genetics with at least 6.50/10.00 or 65% marks. iii. Ph.D. in the relevant field with minimum OCPA 6.50/10.00 or 65% marks
Pay Scale : Rs.24000/-
Application Fee : A Bank Draft of Rs. 200/- in favour of Comptroller, Punjab Agricultural University, Ludhiana

How to apply
Walk in Interview will be held on 26.09.2016 at 11:30 a.m. in the office of the Director, School of Agricultural Biotechnology. No separate information for interview will be sent. No TA/DA will be paid for attending the interview. Candidate Should apply with detailed bio data to this office latest by 19.04.2016

More at http://web.pau.edu/index.php?_act=manageAllBanner&DO=viewAllBanner

Tbl2asn: a command-line program that automates the creation of sequence records for submission to GenBank

Poonam Mahapatra — Mon, 29 May 2017 07:37:08 -0500

Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission.

Tbl2asn is available by anonymous FTP. Copy the right version for your platform, then uncompress the file, rename it to "tbl2asn", and set the permissions, as necessary for the platform.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/