BOL: Related items

Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map

Jit — Wed, 11 Mar 2020 01:12:06 -0500

A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg)

Link to working demo: https://vgteam.github.io/sequenceTubeMap/

Address of the bookmark: https://github.com/vgteam/sequenceTubeMap

Assistant Professor at GAUHATI UNIVERSITY, GUWAHATI

Tue, 16 Dec 2014 01:15:30 -0600

Advt. No.T/2014/4

Ref. No. GU/Estt/T/308(VI)/2014/6451-61

Applications are invited from the Indian citizens for five (5) teaching posts of Assistant Professor (Contractual) under various departments of Gauhati University. Details of the advertisement, other terms and conditions and the application forms are available in the University website www.gauhati.ac.in

Asstt. Professor (Contractual)

2. M.Sc. Microbiology Course in Botany

3 1.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biochemistry (1 post). (Preference will be given to candidates having experience in Biochemistry).

2.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Bioinformatics).

3.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Microbial Genetics).

As per UGC norms

Pay Band & Academic Grade Pay : (Consolidated pay) : Rs. 21,600/- per month

Application Form : Prescribe application form may download from the G.U. website www.gauhati.ac.in

Last date of receipt of filled-in application is 08.01.2015.

Advertisement: www.gauhati.ac.in/openfile.php?file=Notice1258.pdf

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

China University of Macau PhD Position 2015 in Bioinformatics, Computer Science

Mon, 22 Dec 2014 00:12:49 -0600

The Computational Biology and Bioinformatics Group at the University of Macau is inviting applications for PhD Position. Applicants will work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems. The duration of this PhD position is 2-3 years, starting in August 2015. Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month). The applications should be submitted before March 2015.

Study Subject(s): PhD position is award in the field of Bioinformatics/Computer Science.
Course Level: Position is available for pursuing PhD degree level at the University of Macau.
Scholarship Provider: University of Macau
Scholarship can be taken at: China

Eligibility: The ideal candidate would be a master degree holder in Bioinformatics or related disciplines with knowledge in Medical sciences or Life sciences (with GPA of at least 3.0 on a 4-point scale or equivalent) . Knowledge in programming (C and C++) and Linux scripting are necessary; experience in molecular docking, molecular dynamics simulations or molecular modeling is an advantage. The candidate should be fluent in spoken and written English; preference will be given to applicants with good publication records in relevant areas.

Scholarship Open for International Students: Researchers from China can apply for this PhD position.

Scholarship Description:

The Computational Biology and Bioinformatics Group at the University of Macau is looking for a motivated PhD student in Bioinformatics or Computer Science to work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems.

Number of award(s): There is only one PhD position available.

Duration of award(s): The duration of this PhD position is 2-3 years.

What does it cover? Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month).

Selection Criteria: Not Known

Notification: Not Known

How to Apply: Send your current CV, your academic transcripts, a letter of motivation and research interests, two letters of recommendations from academic faculty to Dr. Shirley Siu at shirleysiu[at]umac.mo before March 2015.

Scholarship Application Deadline: The applications should be submitted before March 2015.

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/

JNU Neuroscience/Systems Biology/Mathematical modeling JRF Vacancies

Fri, 26 Dec 2014 11:22:20 -0600

School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi 110067

Recruitment for Project

Applications were invited from the citizens of India for filling up the following temporary position for the CSIR sponsored Fellowship in the School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067. This position is temporary for a period of two and half years or tenable only for the duration of the project. The requisite qualifications & experience are given below.

Project Title : "Understanding Complex dynamics and Information processing in Brain Networks"
Funding Agency : CSIR

Principal Investigator : Dr. R.K. Brojen Singh

Position : Junior Research Fellow(One post)

Salary : As per CSIR rules and guidelines for JRF.

Qualifications & Experience : M.Sc. in Physics/Mathematics/Biology/B.Tech. In Eng. Physics/Comp. Sc. and desirable CSIR-UGC NET Qualified. Candidates should also have at least one years research experience after M. Sc./B.Tech. in works related to Neuroscience/Mathematical modeling.

Candidates possessing requisite qualifications may apply either on plain paper stating the project title along with CV and send to the following address or send as email attachment (pdf or word format) so as to reach on or before 8 January, 2014.

Dr. R.K. Brojen Singh
School of Computational and Integrative Sciences
Jawharlal Nehru University
New Delhi 110067
Email: brojen@jnu.ac.in, brojen@mail.jnu.ac.in

Scripts for the analysis of HGT in genome sequence data.

Jit — Wed, 29 Nov 2017 16:44:10 -0600

Scripts for the analysis of HGT in genome sequence data

Address of the bookmark: https://github.com/reubwn/hgt

Ancestral sequence reconstruction steps !

Surabhi Chaudhary — Fri, 18 May 2018 08:28:26 -0500

Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the study of molecular evolution. The method consists of the synthesis of an ancestral gene and expression of the corresponding ancestral protein. The idea of protein 'resurrection' was suggested in 1963 by Pauling and Zuckerkandl. Some early efforts were made in the eighties-nineties, led by the laboratory of Steven A. Benner, showing the potential of this technique – one that only started to be fulfilled in the post-genomic era. Thanks to the improvement of algorithms and of better sequencing and synthesis techniques, the method was developed further in the early 2000s to allow the resurrection of a greater variety of and much more ancient genes. Over the last decade, ancestral protein resurrection has developed as a strategy to reveal the mechanisms and dynamics of protein evolution.

BEAST is the best way to predict the ancestral structure. but, I suggest following steps?

1- Alignments "Mafft - http://mafft.cbrc.jp/alignment/software/source.html"

mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta > Dataset_Alig.fasta

2- Your dataset has a good phylogenetic signal, is possible to perform with Tree-Puzzle "http://www.tree-puzzle.de";

3 - This dataset which the saturation index, I perform with "http://dambe.bio.uottawa.ca/dambe.asp";

4- Has evidence of possible recombination in your dataset, the evaluate if this presence or absence, because this may to influence the grouping of clades, I perform with

---recombination

4.1- Phi-test, implemented in SplitTree4"http://www.splitstree.org", (.nex file)

4.2- GARD deployed in webserver in the DataMonkey "http://www.datamonkey.org/" - turning to the amino acid seaview -> view proteins -> save as ...) Ideally do a tree-based groups.

4.3- RDP4 for download and installation on Windows in "http://web.cbio.uct.ac.za/~darren/rdp.html"

4.4- Hyphy (Mac, Windows, Linux) in "http://hyphy.org/w/index.php/Download"

4.5- Path-o-Gen (temporal structure of a tree input file -> arquivo.tre)

These steps above, I call of pre-processing to inferences phylogenetic...

5- Perform phylogenetic tree, used Bayesian Inference with Molecular Clock, but is necessary Clock Testing:

- This step is performed with program Beast (Beauti, Beast and TreeAnnotator), and Tracer_v1.5 more FigTree to inspection.

- Tutorials: http://beast.bio.ed.ac.uk/tutorials

- Downloads: http://beast.bio.ed.ac.uk/downloads

Illumina Smartphone Chip !!!

Robert M Willioms — Tue, 30 Dec 2014 23:19:54 -0600

Illumina, the company that claims it brought human genome sequencing down to $1000 prices, has now turned its attention to a consumer product - a chip that you can plug into your smartphone and have it read your genetic information.

The biggest challenge ahead of Illumina is simplifying the process of genetic sequencing. Currently, Illumina’s DNA sequencers are gigantic machines that use techinques like colorimetry to work, but while the core technology is computational, it takes some 30 steps to extract genetic data and run it through. This process will likely have to be hugely simplified on mobile devices, given the fact that some studies require extracting 10 mililiters of blood. Illumina researchers are also working on finding the optimal technology for this on-chip DNA sequencing - be it electrical, optical, or other.

Illumina is one of the most prominent names in genetics, often said to be the Intel of genetic sequencing, as just like Intel it provides the algorithms, the processing brain that runs a DNA reading task.

In other recent smartphone-related biotech news, drug company Pfizer launched its REMOTE project, a new type of clinical trial that does not require going to a hospital for checks - targeted at patients with overactive bladder problems, the FDA-approved REMOTE project allowed to gather data from patients from over 10 states remotely, via mobile devices.

This is indeed the Illumina answer to Apple's Health app, HealthBook, Google HealthFit.

Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore

Neel — Fri, 19 Oct 2018 08:48:43 -0500

Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCONwhile producing contigs of comparable base accuracy.

Address of the bookmark: https://github.com/ruanjue/wtdbg2