#Find all occurrences of a pattern in a string.
#Given: Strings Pattern and Genome.
#Return: All starting positions in Genome where Pattern appears as a substring. Use 0-based indexing.

use strict;
use warnings;

my $string="GATATATGCATATACTT";
my $subStr="ATAT";
my $kmer=length($subStr);

kmerMatch ($string, $subStr, $kmer);

sub kmerMatch { #Check the exact matching kmers with sliding window
my ($string, $myStr, $kmer)=@_;
for (my $aa=0; $aa<=(length($string)-$kmer); $aa++) {
    my $myWin=substr  $string, $aa,$kmer;
    if ($myWin eq $myStr) {
        #print "$myWin eq $myStr\n";
        print $aa;
    }
}
}

• Expansion of Protists and Fungi with hundreds of annotated genomes
• Variation data for bread wheat, rice, Aedes aegypti, and Ixodes scapularis
• Whole genome alignments for O. longistaminata and T. cacao
• Non-coding RNA gene models in Bacteria
• New assembly of tomato (version 2.50)
• Full support for UCSC Track Hub format for hosting your own data in Ensembl

More at http://www.ensembl.info/blog/2015/06/16/ensembl-genomes-release-27-is-out/

http://www.stratosgenomics.com/stratos-genomics-technology

The next-generation sequencing included whole genome sequencing(WGS), transcriptome sequencing (whole cDNA sequencing, RNA-seq), digital gene expression sequencing (Tag-Seq), ChIP-Seq, and so on. And there are many sequencing platform to generate sequece, as well know Sanger/ABi(the frist generation), Solexa/illumina, SOLiD/ABi, 454/Roche. But thier sequence format is different, also they have different error type. High quality data is very important for further analysis or data mining. There are many pipeline for raw sequence quality analysis and control with few of process for reporting reads quality statistical details, trimming, filtering, and error correction. Please bookmarks them for the benefits of bioinformatics community.

https://code.google.com/p/biowiki/

https://code.google.com/p/ngs-pipeline/source/browse/#svn%2Ftrunk

NGSand Perl scripts https://code.google.com/hosting/search?q=NGS+perl&projectsearch=Search+projects

NGS and Python scripts https://code.google.com/hosting/search?q=NGS+Python&projectsearch=Search+projects

Address of the bookmark: https://code.google.com/hosting/search?q=bioinformatics&sa=Search

While your PhD or PostDoc application, it is more common that you got rejected by many professors. Don't disappoint reply it calmly.

In grad school, I shared a house with three Bioinformatics PhD students. One, when he applied to a particular professor, received a letter that said, essentially, "If you are applying because you want to enrich yourself, great. If you are applying because you want a job, you should know that you won't get one." I am trying to tell you this is because if you, with a good background in Bioinformatics, are passing up opportunities, you must be a strong candidate in many areas. Enrich yourself.

So, my suggestion is take a deep breath, forgot about all. Don’t take it personally. It's been usual processes while hunting for a good lab and professor. Take is positive, I am not sure why they reject, but don't worry perhaps the lab don't deserve you. Always remember there are billions of reasons not to hire someone for projects, especially in a research sector.

My suggestion, please do not whine about how you were a great research candidate for the post, and you just can't understand why they were so stupid as to have rejected you! This feeling will not win you any points in research, community. Especially, when in todays socially connected era everyone is linked. Remember, a nice E-mail saying, "I really wished to working with you on this project and I hope we cross paths again," is all you need to send to the professor. Send a thank you note to the professor. Thank them for the time they spend to judge you. In the future, If you and the professor (of your dream) are attending a bioinformatics conference, invite him/her to lunch (please remember to pay the bill). In today evolving scientific ere, always remember to build your solid network in order to get a job of interest. Join all possible networking sites like LinkedIn, ResearchGate, Acamedia, FB for the same reason. You as a researcher always build a bridge with student/researcher/colleague/professor who have the research potential to lead in research and hire you. Just because you didn't get this project, doesn't mean there isn't another that will open up in couple of month.

Mostly, jobs that are hard to get are hard to get. Only you can decide if the continued sacrifices are worth the expected payout. If it is, keep on plowing. Build relationships. Attend conferences.

Image ref @ JaSonYa

Bioinformatics supports to researchers
Customized training in Bioinformatics for researchers and faculty members
Support in Installing, implementing and maintaining software on computer.
Create awareness for taking preventive measure against data security
Organize workshops on thrust ares of Bioinformatics
Research Training to students of Biotechnology and Bioinformatics

More at http://bioinfo.bisr.res.in/index.php

Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of JRF (1) and Project Assistant (1) in DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE as per DBT sanction order and norms.

(i) JRF(1 no.):

Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/ Biochemistry/ Biotechnology/ Bioinformatics;

Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis

(ii) Project Assistant (1 no.):

Qualifications: Graduation in Science,

Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service. Prof. Pramod Tandon, PI/Mr. Devendra Kumar Biswal (Co-PI) email: bicnehu@gmail.com

Advertisement: www.nehu.ac.in/Advertisements/BIC_AdvtPV_030815.pdf

The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:

Research Associate:

-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.

-Familiarity with bioinformatics tools, database development, programming skills

-Minimum 1 publication in any peer reviewed journal

Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.

Working with other members of the TNDRG you will analyse complex genomic and epidemiological datasets, evaluating which computational tools are most suitable. You will contribute to the generation of innovative tools for linking epidemiological and multilevel omics datasets, ensuring that computer programs are written in a form that other collaborators can use and expand.

You will have or be close to completion of a PhD in either: bioinformatics; neuroscience; machine learning; statistics; epidemiology; neurology; or other relevant field. You will have experience programming on either R, Matlab, Python, C++, Java or any other imperative, object oriented or functional language.

Please direct Informal enquiries to Dr Alejo Nevado-Holgado (alejo.nevado-holgado@psych.ox.ac.uk).

You will be required to upload a supporting statement explaining how you meet the selection criteria for the post, a CV, and details of two referees as part of your online application.

The closing date for applications is 12.00 midday on 2 September 2015. Interviews will be held on Tuesday 15 September 2015.

https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118696

Junagadh Agricultural University has given a recruitment notification to fill the posts of Senior, Junior Research Fellows in the establishment.

Name & No: of Posts:

1. Senior Research Fellow: 05
2. Junior Research Fellow: 05

Title of the Projects under Senior Research Fellow:

1. Molecular mapping of important traits and their transfer through marker assisted selection in Groundnut and cotton
2. Aflatoxin and its management in groundnut at Saurashtra region of Gujarat.
3. Improvement in Agricultural Production through nanotechnological inventions at Junagadh.
4. Synthesis and Characterisation of chitosan based NPK-Nano fertilizers

Title of the Projects under Junior Research Fellow:

1. Improvement in Agricultural Production Through Nanotechnological Inventions at Junagadh.
2. Synthesis and Characterisation of chitosan based NPK-Nano fertilizers

Required Eligibility Criteria:

1. Senior Research Fellow:

Age Limit: Candidates age must be maximum 35 years
Educational Qualification: M.Sc in Nanotechnology/Biotechnology/Bioinformatics
Salary: Rs. 16,000/- + HRA for first and second year, Rs. 18,000/- + HRA during third year

2. Junior Research Fellow:

Age Limit: Candidates age must be maximum 30 years
Educational Qualification: B.Sc or M.Sc degree in the field of Nanotechnology/Biotechnology
Salary: Rs. 9,600/- , Rs. 14,400/- p.m

Eligible candidates may attend the walk-in-interview on 10-09-2015 with necessary certificates of testimonials

Click Here for Detailed Recruitment Notification
http://www.jau.in/attachments/Advt/BiotechSRFJRF.pdf