BOL: Related items

TMAP - torrent mapping alignment program General Notes

Poonam Mahapatra — Sun, 02 Apr 2017 15:53:47 -0500

TMAP - torrent mapping alignment program General Notes

TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

The latest TMAP is unsupported. To use a supported version, please see the TMAP version associated with a Torrent Suite release below.

Get the latest source code:

git clone git://github.com/iontorrent/TMAP.git
 cd TMAP
 git submodule init
 git submodule update

https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

Address of the bookmark: https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

Lifemap

Jit — Mon, 10 Apr 2017 05:42:37 -0500

Lifemap is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in Lifemap is similar to the one used in cartography with tools like Google Maps© or Open Street Maps: exploring is done by zooming and panning.

The current tree contains ALL species present in NCBI taxonomy as of October 18th, 2016: 1,135,169 species including 10,545 Archaea, 418,777 Bacteria and 705,847 Eukaryotes. The Lifemap tree is updated every two weeks.

All the nodes in the tree are clickable. This displays various information and options:

The species name (and the associated common name if there is one)
The rank (kingdom, family, class, species...)
Ability to go to the corresponding node/species on NCBI web site (displayed in a new window)
Possibility to download the corresponding subtree in newick extended format
Possibilty to get the whole lineage from the current node/tip to the root of the tree.

Address of the bookmark: http://lifemap-ncbi.univ-lyon1.fr/

Synteny Portal: a web-based application portal for synteny block analysis

Jit — Wed, 24 May 2017 10:39:23 -0500

Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.

http://bioinfo.konkuk.ac.kr/synteny_portal/

Address of the bookmark: http://bioinfo.konkuk.ac.kr/synteny_portal/

RA Bioinformatics at JNU, New Delhi, INDIA

Thu, 27 Apr 2017 03:29:58 -0500

School of Computational & Integrative Sciences
Jawaharlal Nehru University
New Delhi-110067, INDIA

Date: April 24th. 2017 Last Date: May 6th 2017
PROJECT ID: 632

The following posts are urgently required to be filled for the Department of Biotechnology, Government of India funded project jointly running with IIIT-Hyderabad & JNU, entitled "Computational Core for Plant Metabolomics" administrated by Prof Indira Ghosh, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067.
NB: For all the posts, preference will be given to candidates with a good knowledge of Python and/or R in UNIX platform , knowledge of JAVA will also get a special consideration.

1. RA / Research Associate (Metabolic engineering/Computational Biologist)

Salary: Rs. 36000/- + HRA

Vacancy: 1

Essential Qualifications: PhD in Bioinformatics /Mathematics/Computer Science with experience in analyzing high throughput omics-based data/Analysis of Network Biology/Chemoinformatics/Computational Biology related Software development. Published paper in the field is a must to prove the experience. Special consideration will be given if have experience in Industry, teaching & product development.

Desired Skills: Prior experience in handling and guiding bioinformatics, metabolomics data, planning of new research area in metabolic driven network , collaborating with industry , preparing and filing reports etc. Will be expected to communicate with user groups and coordinate with LIMS group in Hyderabad and the Cheminformatics group in Delhi.

2. Project SRF (Network model building/Systems biology integration)

Salary*: Rs.18000/- + HRA

Vacancy: 1

Essential Qualifications: M.Tech in Computational Biology with project experience or Masters / B.Tech in Basic Sciences with at least 2yrs of research experience in Bioinformatics/Mathematical Model building using Computational Biology tools & related Database / Network analysis etc. For M.Sc/B.Tech, Published paper in peer-reviewed Journal whereas for M.Tech, the degree obtained in computational biology is a must.

Desired Skills: Will be expected to manage ongoing research activities in LIMS, interact with LIMS group, build network model using data compiled by experimentalist, prepare and file reports and associated project work etc. Familiarity with plant systems biology and genomics /metabolite resources related to plant metabolomics is desirable.

More at http://www.jnu.ac.in/Career/currentjobs.htm

SOAP2 : Short Oligonucleotide Analysis Package 2

Poonam Mahapatra — Wed, 23 May 2018 10:09:22 -0500

SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).

Address of the bookmark: http://soap.genomics.org.cn/soapaligner.html

S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences

Abhimanyu Singh — Tue, 02 Oct 2018 17:57:27 -0500

S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can be efficiently compared. The tool includes functionality to extract, analyze, and automate BLAST queries of regions of interest within the heatmap. This facilitates the investigation of quickly evolving coding regions, novel coding regions, and laterally transferred elements.

Address of the bookmark: https://bitbucket.org/lkalesinskas/splot

Bienko and Crosetto Labs

Fri, 12 May 2017 07:42:15 -0500

We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation to gene expression regulation. The Crosetto group engineers new molecular methods for single-cell and spatially resolved omic measurements of DNA, RNA, and proteins, with a strong focus on tumor heterogeneity. By sharing ideas and resources, we work synergistically towards a more quantitative understanding of life’s processes in healthy and diseased conditions.

https://bienkocrosettolabs.org/

JRF/SRF / Project Assistant-II recruitment in National Agri-Food Biotechnology Institute (NABI)

Mon, 15 May 2017 05:37:52 -0500

National Agri-Food Biotechnology Institute
ADVT. No: 2017-Researcher (02)

JRF/SRF / Project Assistant-II recruitment in National Agri-Food Biotechnology Institute (NABI)

Essential Qualification: According to the DST (DST OM No.SR/S9/Z-09/2012 dated 21.10.2014) Post Graduate degree in basic science(M.Sc) in Bioinformatics/Computational Biology/Systems Biology/Information Technology with NET or Graduate degree in professional course with NET or Post Graduate Degree (M.Tech) in professional course in Bioinformatics/Computational Biology/Systems Biology/Information Technology. Desirable qualification/skills: 1) Should be proficient in programming in Perl/Python/R language etc. 2) Should have knowledge and skills for data mining in biological sequence database . sequence analysis tools/packages, NGS Analysis . 3) Should have knowledge and skills to work in linux environment and write shell scripts.

Age : 28 years

Hiring Process : Written-test
Job Role : Research/JRF/SRF
How to apply

Application should be sent to Administrative officer, National Agri-Food Biotechnology Institute, Knowledge City, Sector-81, Mohali so as to reach latest by 30.05.2017 before 5:30 pm.

More at http://www.nabi.res.in/Vacancies/NABI/ResearchFellowships/JRFSRFRA/2017/ADVT.%20No%202017Researcher%20(02)/ApplicationForm.pdf

Pango Lineage Analysis !

Abhi — Mon, 15 Nov 2021 03:38:29 -0600

The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by researchers to perform analyses on SARS-COV-2 sequence data.

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html

SeqCAT: Sequence Conversion and Analysis Toolbox

Neel — Fri, 14 Jun 2024 14:36:53 -0500

Your all-in-one solution for smooth conversion of sequence coordinates.

Designed for bioinformatics data analysis and daily laboratory work, SeqCAT simplifies sequence coordinate conversion. Extract gene and transcript information, manipulate sequences, and easily validate complex genetic events such as fusions with SeqCAT.

More at https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae422/7683049?login=false

Address of the bookmark: https://mtb.bioinf.med.uni-goettingen.de/SeqCAT/home