Credits

Plant Genome pipelines and analysis systems are using a number of publicly available software tools. Their availability and value is gratefully acknowledged:

1. GBrowse - a combination of database and interactive web pages for manipulating and displaying annotations on genomes.
2. Vista tools - full scaffold alignments and visualization of comparative data for the plant genomes in Phytozome.
   VISTA alignment pipeline includes the following modules:
   • BLAT - local alignment program to find a set of anchors for the whole-genome alignment;
   • Shuffle-LAGAN - global alignment framework allowing to find rearrangements (inversions, transpositions and some duplications);
   • PROLAGAN - progressive multiple alignment program for genome assemblies;
3. Arachne - Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. 2003 Jan;13(1):91-6.
4. All Paths LG - Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8.
5. GenomeScan - Yeh RF, Lim LP, Burge CB. Computational inference of homologous gene structures in the human genome. Genome Res. 2001 May;11(5):803-16.
6. FgenesH - Salamov AA, Solovyev VV. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 2000 Apr;10(4):516-22.
7. Augustus - Stanke M, Tzvetkova A, Morgenstern B. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol. 2006;7 Suppl 1:S11.1-8.
8. BWA - Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010 Mar 1;26(5):589-95. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15;25(14):1754-60.
9. SAMTools - Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9.
10. TopHat/CuffLinks - Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012 Mar 1;7(3):562-78.
11. PASA - Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003 Oct 1;31(19):5654-66.
12. BLAT - Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.
13. Exonerate - Slater GS, Birney E. Automated generation of heuristics for biologica sequence comparison. BMC Bioinformatics. 2005 Feb 15;6:31.
14. JalView - Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009 May 1;25(9):1189-91.
15. BLAST - Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009 May 1;25(9):1189-91.
16. BioMart - Smedley D, Haider S,Ballester B,Holland R,London D,Thorisson G, Kasprzyk A ., BioMart–biological queries made easy. BMC Genomics 2009;10:22.
17. HMMER - Eddy SR, A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009;23:205-211.
18. MUSCLE - Edgar RC, MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-1797.