Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).

GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).

KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).

Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).

MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).

R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).

SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).

Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).

- Plan more efficient experiments
- Correctly interpret results
- Communicate results in publications more effectively

The course focus is on methodologies, not on particular software tools. After the course participants should be able to apply the methods in their respective environment. However, during the course, hands-on sessions will be performed using the Genedata Expressionist® software, which enables participants to quickly apply the discussed methods and visualize results. No previous knowledge on Expressionist® is required; access to the software is free of charge during the course.

More @ http://www.dixa-fp7.eu/dixa-training/dixa-training-agenda/genedata-academy#!

Postdoc position (m/w/d)

in the field of computational evolutionary microbiology is available
for an initially limited period of 36 months at the earliest possible
date. The weekly working time corresponds to 100% of full employment
(If the legal requirements under collective bargaining law are met, the
tariff grouping is carried out up to pay scale 13 TV-L. The obligation
to teach amounts to 4 hours.

The Genomic Microbiology Group research interests are focused on
microbial genome evolution with an emphasis on the study of lateral gene
transfer. In our research we use both computational and experimental
approaches (see www.uni-kiel.de/genomik). The position offers the
opportunity to develop an independent research profile within the group
research focus. The successful applicant is expected to be involved
in teaching of bioinformatics and molecular evolution, including the
development of teaching materials (lectures/exercises/short videos).

Your profile:
· Doctoral or PhD degree in Molecular Evolution, Bioinformatics or
related fields.
· Knowledge and experience in programming (e.g., Python) and
biostatistical analysis (e.g., with R or MatLab).
· Any of the following expertise is an advantage: the analysis of
genomic or transcriptomic data, phylogenetic reconstruction,
comparative genomics.
· Good oral and written communication skills in English.
· Ability to teach in German is an advantage (alternatively, an
indication to do so from the 2nd year on).
· Skills and motivation to communicate and interact with other
scientists.

The Christian-Albrechts-University sees itself as a modern and
cosmopolitan employer. We welcome your application regardless of your age,
gender, cultural and social background, religion, ideology, disability
or sexual identity. We promote equality of the sexes.

The Christian-Albrechts-University is committed to the employment of
people with disabilities. Preference will be given to applications from
severely handicapped persons and persons of equal standing, provided
they are suitable.

We expressly welcome applications from people with a migration background.

For enquiries regarding the position, teaching obligations and research
topic please contact Prof. Tal Dagan: tdagan@ifam.uni-kiel.de.

Applications should be submitted by email to Mrs. Haacks
(dhaacks@ifam.uni-kiel.de) as a single PDF and include: (1) a letter of
motivation (max 1 page, Arial 11, line spacing 1.15), (2) CV, (3) PhD
certificate. Please use 'GMG postdoc application - [your name]'
as a subject.

Please, refrain from sending us application photos.

Application deadline: August 31 2021 or until the position is
filled. Interviews will take place during September/October 2021. The
planned starting date for the position is flexible (but in 2021).

Now my main interests are in gene regulation, where we work on promoter analysis; non-coding RNA, where miRNAs and structure prediction are the main areas; and protein structure, where the group is working on methods for structure prediction from sequence. To read more about these topics, please see the research pages.

Lab page @ http://wiki.binf.ku.dk/User:Krogh

1. NCBI (National Center for Biotechnology Information):

   • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
   • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
   • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
   • You can download sequences individually or in batches using the provided tools.

2. GreenGenes:

   • GreenGenes is a widely used 16S rRNA gene sequence database.
   • You can access it at http://greengenes.secondgenome.com/.
   • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

3. SILVA:

   • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
   • It covers not only 16S rRNA but also other ribosomal RNA sequences.
   • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

4. Ribosomal Database Project (RDP):

   • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
   • It provides tools for sequence analysis and classification.
   • You can download sequences and taxonomy information from their website.

5. QIIME (Quantitative Insights Into Microbial Ecology):

   • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
   • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
   • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

Salary: Rs. 10,000/- per month.

Age limit: 35 for men and 40 for women & SC/ST.

Qualification: First class in M. Sc (Agriculture)/MCA/M.Sc (IT)/ M. Sc (Computer Application)/M.Sc (Bioinformatics)/M.Sc (Geoinformatics).

Desirable: Two years experience in web design and web programming.

Date & time of interview: 08.10.2013, 10 am

Interested candidates may appear for an interview at this institute along with their application in plain paper containing the following particulars viz. (1) Name (2) Father/Husband/Guardian’s Name (3) date of birth & age as on 01.10.2013 (4) Permanent address (5) Address for communication (6) Email address and Telephone No. with code (7) Qualification (8) National fellowship like ICAR/CSIR/UGC etc. if any (9) Whether SC/ST/OBC (10) Details of experience (Attested copies of degree certificate, proof of age, mark sheets). Original certificates should be produced for verification.

No TA/DA will be admissible to the candidates attending the test. The selected candidate will have to join immediately.

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https://gold.jgi.doe.gov/

Address of the bookmark: https://gold.jgi.doe.gov/

The course Bioinformatics Algorithms (Part 1) by Pavel Pevzner, Phillip E. C. Compeau, and Nikolay Vyahhi from University of California, San Diego will be offered free of charge to everyone on the Coursera platform. Sign up at http://www.coursera.org/course/bioinformatics.

https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Address of the bookmark: https://www.hiv.lanl.gov/components/sequence/HIV/search/search.html

Walk-in-Interview

Walk-in-interview will be held on October 5, 2013 at 10:00 A.M. at IASRI, New Delhi for a project “A New Distributed Computing Framework for Data Mining” funded by Department of Electronics and Information Technology, Government of India for the following posts. The appointment will be on contractual basis upto 14th October, 2015 or till the termination of the project whichever is earlier and the incumbent shall not have any claim for regular appointment under ICAR.

Research Associate

Ph.D. in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent or

Post-Graduation in Bioinformatics/ Agricultural Statistics/ Statistics/ Computer Science/ Computer Application or equivalent with 1st Division and at least two years of research experience

 Knowledge of Statistical Analysis /Bioinformatics tools for computational genomics.

 Knowledge of R/Perl programming language

Research Associate

Ph.D. in Computer Science/ Computer Application / Bioinformatics/ Agricultural
Statistics/ Statistics or equivalent or

Post-Graduation in Computer Science/ Computer Application /Bioinformatics/ Agricultural Statistics/ Statistics or equivalent with 1st Division and at least two years of research experience

 Expertise in Java programming.
 Knowledge of system administration and networking under Linux environment.
 Knowledge of parallel programming and cluster computing.

Emoluments for Research Associate: Consolidated Rs:24000/- per month + HRA (for Ph.D. Degree holders) and Rs:23000/- per month + HRA (for Master’s Degree holders)

Age Limit: Age should be not more than 40 years (5 years relaxation for SC/ST/women candidates and 3 years for OBC candidates as on date of interview).

Interested candidates are requested to appear for Walk-in-Interview on the date and time as specified above in Room No. 106, Training Cum Administrative Block of the Institute along with their application giving bio-data with attested copies of certificates, degrees, testimonials, etc. and one passport size photograph.

Original certificates/ Degrees are needed to be produced at the time of interview.

No T.A. /D.A. will be paid for appearing in the interview.

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