Address of the bookmark: https://forge.ird.fr/diade/dynadiv/grannot

YASRA uses LASTZ (http://bx.psu.edu/miller_lab for released version and http://www.bx.psu.edu/~rsharris/lastz/newer for newer version) for aligning the sequences to the reference genome. Please install LASTZ (the newest version on http://www.bx.psu.edu/~rsharris/lastz/newer) and add the LASTZ binary in your executable/binary search path before installing YASRA.

Address of the bookmark: https://github.com/aakrosh/YASRA

Prokka – Standalone command line tool, takes just a few minutes per genome. This is the best way to get good quality annotation in a flash, which is particularly useful if you have loads of genomes or need to annotate a pangenome or metagenome. Note however that the quality of functional information is not as good as RAST, and you will need several extra steps if you want to do functional profiling and pathway analysis of your genome(s)… which is in-built in RAST.

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

PGAP: NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume.  NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

BEACON (automated tool for Bacterial GEnome Annotation ComparisON), a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.

BlastKOLA: Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to this server and can be executed in an interactive mode. BlastKOALA is suitable for annotating fully sequenced genomes.

PAGIT: Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.

MAKER: A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).

MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

Applications are invited for:

Junior Research Fellow, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: M.Sc. (preferably in Biotechnology, Life Sciences or Zoology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference. Bioinformatics expertise required.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.

Research Associate, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi

Qualifications:

Education: Ph.D. (in Biology, Biotechnology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference.

Fellowship: As per DBT guidelines.

Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.

Closing date for applications: 04/03/2017

Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.

Address of the bookmark: http://mitos.bioinf.uni-leipzig.de/index.py

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome

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

Address of the bookmark: http://ritchielab.psu.edu/software/phenogram-downloads

https://github.com/tanghaibao/jcvi

More at https://github.com/tanghaibao/jcvi/wiki

Address of the bookmark: https://github.com/tanghaibao/jcvi

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements.

Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics
Knowledge in computer programming, LINUX OS.
Expertise in use of R/other Bioinformatics software

More at http://iasri.res.in/employment/2017/cabin_advertisement_RA_SRF_YP_Mar2017.pdf

Phenomics of Moisture Deficit Stress Tolerance and Nitrogen Use December 31, 2019

Research Associate (RA) Two (2)

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or System Administrator/ Computer expert for database development, development of phenome data bank and virtual phenomics facility, data archiving and Efficiency in Rice and Wheat-Phase II (Funded by National Agricultural Science Fund, ICAR) Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements. maintenance; Development of image analysis algorithms, APIs and IAPs.

Knowledge in System Biology/ Statistical and computational Genomics/ Bioinformatics
Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software & tools.
December 31, 2019

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science / Computer Application or equivalent or Master’s in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 4 years or 5 years of Bachelor’s degree having 1st Division or 60% marks or equivalent overall grade point average, with at least two years of research experience as evidenced from fellowship/ associateship/ training/ other engagements.

Knowledge of Statistical and Computational Genomics/ Bioinformatics.
Knowledge of programming in LINUX/R/Perl/JAVA/PHP/JSP and use of various software & tools.
March 31, 2020