Tools

• Parsnp - Core-genome alignment and analysis
• Gingr - Interactive visualization of alignments, trees and variants
• HarvestTools - Archiving and postprocessing

Address of the bookmark: https://harvest.readthedocs.io/en/latest/

Project: Indo-UK Centre for improvement of Nitrogen use efficiency in wheat Dr. Soma S. Marla, Pr. Scientist (Bioinformatics), Division of Genomic Resources, ICAR, NBPGR, ND.

Qualification: Ph.D. Degree in Computer Sciences/Bioinformatics OR 1. First class Master’s degree in any discipline of Plant Sciences with specialization in Computer Sciences/ Bioinformatics having 1st division or 60% marks or equivalent overall grade point average with at least two years of research experience as evidenced from Fellowship/ Associate ship. 2. NET qualification is essential for the candidates with 3+2 years B.Sc.+ M.Sc. Desirable: Demonstrated experience & skills in database design, management, UNIX OS, in NGS data analysis. Experience substantiated by publications of high quality will be preferred.

No.of Post: 1

Pay Scale: Rs. 40,000 (Ph.D)/ Rs + 30 % HRA; Rs.38,000 ( Masters Degree 0 + 30 % HRA).

Age Limit : below 40 years for RA position
How to apply
Applicants for RA post should send their complete CV (Advance copy of the application may be sent by email to :soma.marla@icar.gov.in or ssmarl@yahoo.com, should enclose the copy of the research publications; one page summary of their achievement relevant to the post applied for; and should enclose two reference letters (one must be from the person with whom worked latest). Shortlisted candidate will be intimated for interview by email.

The candidates who wish to attend the walk-in interview are requested to bring with them five copies of the CV (one copy with photograph) as per the format given below. Also, the candidates should bring the original documents such as degree certificates, marks sheets, publications, thesis, experience certificate etc. for verification.

Date of Interview: 17.8.2016.

More at http://www.nbpgr.ernet.in/Downloadfile.aspx?EntryId=7133

Applications are invited on plain paper from eligible candidates along with biodata and copies of certificates in support of age, qualification and experience for the following position:

Particulars Description

1. Position & No. JRF (Junior Research Fellow) 01

2. Title of the Project Molecular modeling and docking studies on Deguelin and its derivatives with cell cycle arrest, apoptosis and anti-angiogenesis pathway proteins in cancer cell signaling pathway

3. Tenure 3 years

4. Investigator Dr. K. V.Swamy

5. Institute Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Tathawade, Pune 411033.

5. Qualifications/Eligibility

Essential: NET (National Eligibility Test) qualified M. Sc Bioinformatics/ M. Tech Bioinformatics/M. Sc Biotechnology/M. Tech Biotechnology or Graduate degree in Professional course with NET qualification or Post graduation degree in professional course

The following examinations conducted by various Central Government Departments/Agencies are considered as National Eligibility Test (NET).

1. CSIR-UGC-LS
2. GATE (Graduate Aptitude Test in Engineering)
3. JAM (Joint Admission Test)
4. GPAT (Graduate Pharmacy Aptitude Test)
5. BET(Biotechnology Eligibility Test)
6. BINC(Bioinformatics National Consortium)
7. JEST( Joint Entrance Screening Test)
8. JGEEBILS(Joint Graduate Entrance Examination for Biology & Interdisciplinary Life Sciences)
9. NBHM Ph.D scholarship Screening Test
10. ICMR- JRF Entrance Examination
11. AICE (ICAR-All India competitive Examination )
(For all above examinations valid score considered at the time of interview)

Desirable: Knowledge and skills in Bioinformatics tools/ softwares

6. Monthly Emoluments Rs.25,000/ (As per DST-SERB rules)

7. Last date for submission of prescribed application 20/08/2016

Kindly send your applications to “Dr. K. V. Swamy, Asst.Professor, Dr. D. Y. Patil Biotechnology & Bioinformatics Institute, Survey No. 87/88, Mumbai-Pune Express Way, Tathawade, Pune - 411033, Maharashtra, India”. Highlight the envelope with “Application for post of JRF (Junior Research Fellow)”.

Note: No TA/DA will be paid for attending the interview.

Advertisement: http://careers.dpu.edu.in/Biotech.aspx

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

unzip blatSrc35.zip

to unpack the archive. This gives a directory blatSrc now move into that directory.

#cd blatSrc

before you begin read the README file that comes with the source code.

One thing about building blat is that you need to set the MACHTYPE variable so that the BLAT sources know what type of machine you are compiling the software on.

on most *nix machines, typing

echo $MACHTYPE

will return the machine architecture type.

On my CentOS 6 based system this gave:

x86_64-redhat-linux-gnu

However, what BLAT requires is the 'short value' (ie the first part of the MACHTYPE). To correct this, in the bash shell type (change this to the correct MACHTYPE for your system)

MACHTYPE=x86_64
export MACHTYPE

now running the command:

echo $MACHTYPE

should give the correct short form of the MACHTYPE:

x86_64

now create the directory lib/$MACHTYPE in the source tree. ie:

mkdir lib/$MACHTYPE

For my machine, lib/x86_64 already existed, so I did not have to do this, but this is not the case for all architectures.

The BLAT code assumes that you are compiling BLAT as a non-privileged (ie non-root) user. As a result, you must create the directory for the executables to go into:

mkdir ~/bin/$MACHTYPE

If you are installing as a normal user, edit your .bashrc to add the following (change the x86_64 to be your MACHTYPE):

export PATH=~/bin/x86_64::$PATH

For me, though, this was not good enough. I wanted the executables in /usr/local/bin where all my other code goes. As a result I did some hackery...

There is a master make template in the inc directory called common.mk and I edited this file with the command:

vi inc/common.mk

I replaced the line

    BINDIR=${HOME}/bin/${MACHTYPE}

with

    BINDIR=/usr/local/bin

saved and quit (as this is in my path, I do not need to do anything else)

All the preparation is now done and you can create the blat executables by going into the toplevel of the blat source tree (for me it was /usr/local/src/blat/blatSrc, but change to wherever you unpacked blat into).

Now simply run the command:

make

to compile the code.

Blat installed cleanly and the executables were all neatly placed in /usr/local/bin/x86_64, just like I wanted.

now simply running the command:

blat

on the command line gives me information on blat and sample usage.

Blat is installed and it's installed properly in my system code tree!!!

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign