Dan Kortschak, Bioinformatics Group, School of Molecular and Biomedical Science ,The University of Adelaide

Address of the bookmark: http://talks.biogo.googlecode.com/git/illumination/illumination.pdf

http://www.colorado.edu/news/releases/2013/09/24/new-cu-boulder-led-study-finds-%E2%80%98microbial-clock%E2%80%99-may-help-determine-time

Paper:

http://www.elifesciences.org/wp-content/uploads/2013/09/eLife.01104_INPRESS.pdf

1. rs1426654 SNP of SLC24A5 gene is decider of skin pigmentation variation in South Asia
2. rs1426654-A allele is widely spread throughout the Indian subcontinent 
3. Skin pigmentation is also account by the combination of processes like selection and demographic history of populations affected by their language and origin
4. Sign of positive selection in Europeans, Middle East, Pakistan, Central Asia and North India but not in South India
5. In European , A-allele is almost reached to fixation

Paper:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003912

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

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

Address of the bookmark: http://www.dkfz.de/en/applied-bioinformatics/telomerehunter/telomerehunter.html

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

Here is how I use the blasr to align PacBio reads to the contigs (target.fasta). The “target.fasta.sa” is the suffix array from “target.fasta” generated by sawriter.

blasr query.fa ./target.fasta -sa ./target.fasta.sa -bestn 40 -maxScore -500 -m 4 -nproc 24 -out target.m4 -maxLCPLength 15

the output format option “-m 4″ generate the alignment coordinate. Not fully documented, but I can explain that to you. 

I use a 24 cores / 48G ram server for the alignment. It took about 2 to 3 hours aligning 3G PacBio Reads to 10^6 sequences of short read contigs with a mean 3.5kbp length.

Address of the bookmark: http://bix.ucsd.edu/projects/blasr/

Bachelor/ BS Bioinformatics at
1. Al-khair University, Bhimber
2. Government College University, Faisalabad
3. University Of Agriculture, Faisalabad
4. Comsats Institute Of Information Technology [isb], Islamabad
5. International Islamic University, Islamabad
6. Quaid-e-azam University, Islamabad
7. Khushal Khan Khattak University, Karak
8. Virtual University Of Pakistan, Lahore
9. Virtual University Of Pakistan, Lahore
10. Hazara University, Mansehra
11. Shaheed Benazir Bhutto Women University, Peshawar
12. Comsats Institute Of Information Technology, Sahiwal
13. Capital University Of Science And Technology, Islamabad
14. Foundation University, Islamabad
15. Baqai Medical University/hospital, Karachi
16. Institute Of Business And Technology(main Campus), Karachi
17. Sir Syed University Of Engineering & Technology, Karachi
18. Forman Christian College, Lahore
19. Qarshi University (lhr), Lahore
20. The Superior University, Lahore
21. University Of Management And Technology, Lahore
22. Federal Institute Of Health Sciences, Lahore
23. Shaheed Benazir Bhutto Women University Peshawar, Sub Campus, Swabi
24. Government Postgraduate College ( Mandian), Abbottabad
25. Federal Institute Of Health Sciences, Multan
26. Fedral Institute Of Health Sciences, Muzaffarabad
27. The Limit Institution Of Health Sciences, Sahiwal

Master/ MS Bioinformatics cources at
1. Government College University, Faisalabad
2. Comsats Institute Of Information Technology [isb], Islamabad
3. International Islamic University, Islamabad
4. National University Of Science & Technology, Islamabad
5. Quaid-e-azam University, Islamabad
6. University Of Sindh, Jamshoro
7. Virtual University Of Pakistan, Lahore
8. Hazara University, Mansehra
9. Shaheed Benazir Bhutto Women University, Peshawar
10. Capital University Of Science And Technology, Islamabad
11. Cecos University Of Information Tech. & Emerging Sciences, Peshawar

The real bioinformatics scope lies if there are research labs which work in this field. One has to take account of that. If so then try to get information of those labs and visit them to get a hang of the work they pursue.

There is a huge buzz of precision medicine in light of genomics all around the world. One should also try to see how genomics infrastructure is built up or standing in Pakistan. If research labs having collaboration with hospitals employ genomics then one must also visit such labs. This will bring new avenues in healthcare advances. Not only it opens up the wealth of knowledge one can make out of genomics study but will also advance the critical thinking of therapies.

So I would encourage to target research labs working in the fields and also get information of hospitals employing genomics, this will give you an overall understanding of the fields demand in your country.