Welcome to phylobabble.org, a discussion forum for phylogenetic theory and applications. The primary goal of this forum is to discuss best practice and new developments in phylogenetics. Although we do have a Troubleshooting category for getting feedback on analyses, this is not a help site for running phylogenetics programs.

A great place to chat about phylogenetics for researchers and the broader community of students and science-interested citizens. 

Address of the bookmark: http://phylobabble.org/

The fellowship will be for a period of 3 years, or for a period of 4 years, with 25 % compulsory work (e.g. teaching responsibilities at the department) contingent on the qualifications of the candidate and the teaching needs of the department.

Starting date no later than October 1, 2021.

More at https://www.jobbnorge.no/en/available-jobs/job/199984/phd-research-fellow-in-genomics-and-bioinformatics

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

More at sandbox.bio

Address of the bookmark: http://sandbox.bio

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

• In a GitHub or GitLab repository
• Free to use
• Written in markdown or similar

NOTE: This list of courses is selected only based on the above criteria.
There are no checks on quality.

https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

Address of the bookmark: https://glittr.org/?per_page=25&sort_by=stargazers&sort_direction=desc

WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

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

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

• What is Bioinformatics - An introduction article by Mark Gerstein at Yale University.
• The powerful world of bioinformatics
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• Human Genome Research A description of the Human Genome Project.
• Retooling for Bioinformatics An article from The Scientist
• A Programming Course in Bioinformatics A discussion of the task of teaching an introductory bioinformatics course. By Russ Altman and John Koza.
• Sequence analysis Keith Robison's guide to the exciting world of biosequence comparison! Useful background information on a variety of computational biology algorithms.
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• Understanding the human genome By D. L. Brutlag, in Scientific American: Introduction to Molecular Medicine , P. In Leder, D. A. Clayton, E. Rubenstein, Eds., (New York: Scientific American , 1994), pp. 153-168.
• Viva bioinformatics, but who survives? , 1999.
• Bioinformatics: Playing The Numbers Game June 1999
• Mining the Genome Sept 1999
• Commercialization of biological information and the rise of bioinformatics - Part I , Nov/Dec 1999, 20/21, pp. 40-47.
• Commercialization of biological information and the rise of bioinformatics - Part II , Jan 2000, pp. 51-56.
• Turbo-charging bioinformation for drug discovery , Feb 2000, pp. 38-49.
• Bioinformatics: low supply, high demand June 2000
• The Next Wave of the Genomics Business July 2000
• The Bioinformatics Gold Rush July 2000
• Bioinformatics . Next Wave feature on careers in bioinformatics.September 2000
• A prerequisite for working in thie field: love of computers article from The Scientist (Nov 2000)
• Sep/Oct 2000 issue of the MIT Technology Review
• How to become a bioinformatics expert , including a listing ofEuropean opportunities to study bioinformatics. Compiled by theVirtual School of Natural Sciences BioComputing Division.
• Protein Sequence Alignment and Database Scanning Geoff Barton's review.
• Pattern matching and motifs 
• Knowledge-based Analysis of Microarray Gene Expression Data Using Support Vector Machines
• VHG Virtural HyperGlossary. Defines terms used in different subfields, currently Glycoscience, Protein Structure.
• LASSAP a LArge Scale Sequence compArison Package
• Bioinformatics in pre- and post-genomics eras , Trends in Biotech. ,Vol. 18 , pp. 133-135, April 2000.
• Confluence of Western and Traditional Medicines and Future Prospectes - Part I , Mar/Apr 2000, pp. 34-37.
• Confluence of Western and Traditional Medicines and Future Prospectes - Part II , May/Jun 2000, pp. 66-74.
• Computers + Biology = Bioinformatics April 2001
• Bioinformatics U., Genome Technology, September, 2001 An article from Genome Technology written by Nat Goodman about bioinformatics curricula.
• Training in a Hybrid Discipline, Nature, October 25, 2001 An article from Nature written by Potter Wickare and Paul Smaglik on bioinformatics training programmes in North America.
• Bioinformatics Knowledge Vital to Careers - Competition from mathematicians and computer scientists compels biologists to become computational article from The Scientist (Sept 2002)
• The babel of bioinformatics By Teresa Attwood, Science , 5491: 471 (2000).
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• Are you ready for the revolution? By Declan Butler, Nature , 409: 758-760 (2001).
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• The genome explained By Ellen Licking, Business Week , June 12, 2000.
• Why bioinformatics is hot career By Stacey Wells, San Francisco Chronicle , March 4, 2001.
• Proteomics: Beyond the genome Edited by Patricia O'Connell, Business Week Online, June 7, 2001.
• A true believer dismisses indifference to bioinformatics By Terence Chea, Washington Post , March 14, 2002.
• Genome map on a grain of rice By Kristen Philipkoski, Wired News , March 29, 2002.
• Informatics moves to the head of the class By Beth Schachter, Bio-IT World , June 12, 2002.
• The proteomics odyssey By Malorye Branca, Bio-IT World , Aug. 13, 2002.
• Dell goes nuts for clusters By Michael Kanellos, CNET News.com , Sept. 2, 2002.
• IBM teams with TurboGenomics By Salvatore Salamone, Bio-IT World , Sept. 5, 2002.
• The new, new pharmacogenomics By Malorye Branca, Bio-IT World , Sept. 9, 2002.
• RLX introduces a biocluster in a box By Salvatore Salamone, Bio-IT World , Sept. 17, 2002.
• CombinatorX gets $40 million to look for drug synergies By Salvatore Salamone, Bio-IT World , Sept. 24, 2002.
• Calculating with DNA By Salvatore Salamone, Bio-IT World , October 2002.
• Hitachi Soft develops low-cost human genome DNA chip By Kuriko Miyake, ITworld.com , Oct. 8, 2002.
• IBM chooses Linux for 'Blue Gene' supercomputer By Lisa Gill,NewsFactor Network , Oct. 24, 2002.
• The international 'HapMap' project cbsnews.com , Oct. 29, 2002.
• US stem cell policy deters investors By Steve Mitchell, UPI , Nov. 2, 2002.
• Biochip sprouts DNA strands By Kimberly Patch, Technology Research News , Nov. 13, 2002
• Genomics consolidation � no pain, no gain By Malorye Branca, Bio-IT World , Dec. 10, 2002.
• Data stored in multiplying bacteria By Natasha McDowell,NewScientist.com , Jan. 3, 2003.
• Cowabunga! Scientists to start Bovine Genome Project Science Daily , March 5, 2003.
• Computational Analysis of Complexity in Gene Expression Arrays
• Building your own Bioinformatics Supercomputer for Cheap Using Grid Technology
• Career Advice for Computational Biology By Amjad-Ali Khoja at U. Texas.
• Proceedings of the National Academy of Sciences
• A Practical Guide to protein sequence and structure analysis at UCL

Feel free to add more useful article links below by commenting on this page. Your comments are welcome.