arjunprasad.net

Some links to resources I created or use

• selectRowByCol A little script to do joins on columns of whitespace delimited text files.
• soop: script for picking overgo hypridization probes from blast/blastz alignments.
• ExactPlus: web application and perl script to find short highly conserved regions from multiple sequence alignments.
• fixReadnamesInPosmap: convert internally generated UIDs to read names for Celera Assembler posmap files when assembly data was from FASTQ files.
• prune_newick: a little perl script using BioPerl to remove taxa from newick formatted trees.
• Nilex Morse Tutor: A morse code tutor.
  
  
• Useful links to other resources.
• Some recipes, by popular request.

Publications

• Prasad AB, Allard MW, NISC Comparative Sequencing Program, Green ED. Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Datasets. Molecular Biology and Evolution. 2008 Sep;25(9):1795-808. PDF Supplementary Data
• Antonellis A, Bennett WR, Menheniott TR, Prasad AB, Lee-Lin SQ, Green ED, Paisley D, Kelsh RN, Pavan WJ, Ward A. Deletion of long-range sequences at Sox 10 compromises developmental expression in a mouse model of Waardenburg-Shah (WS4) syndrome. Human Molecular Genetics 2006 Jan 15; 15(2):259-71. PDF
• Portnoy ME, McDermott KJ, Antonellis A, Margulies EH, Prasad AB, Kingsley DM, Green ED, Mortlock, DP. Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer. Genomics 2005 Sept; 86(3):295-305. PDF
• Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber, RJ, Kent WJ, Siepel AC, Karolchik D, Bruen TC, Cutler DJ, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VVB, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang L-H, Osoegawa K, Zhu B, Zhao B, and Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Multi-species sequencing of targeted genomic regions: comparative studies of genome structure, function, and evolution. Nature. 2003 Aug 14; 424: 788-93. PDF
• Thomas JW, Prasad AB, Summers TJ, Lee-Lin SQ, Maduro VV, Idol JR, Ryan JF, Thomas PJ, McDowell JC, Green ED. Parallel construction of orthologous sequence ready clone contig maps in multiple species. Genome Research. 2002 Aug;12(8):1277-85. PDF