Table 8.
Databases and software used
| Version and/or date downloaded | Source | |
|---|---|---|
| Sequence analysis and assembly | ||
| phred | 0.000925.c | 1 |
| Cross match | 0.990319 | 1 |
| Qualtrim | September, 2000 | 2 |
| Simpletrim | July, 2000 | 2 |
| RepeatMasker | July, 2000 | 1 |
| phrap | 0.990319 | 1 |
| CAP3 | July, 2000 | 3 |
| Flip | 2.0 | 4 |
| Sequence similarity searches | ||
| Stand-alone BLAST | Oct., 01 and later | 5 |
| nr | Aug., 2001 | 5 |
| nt | May, 2001 | 5 |
| EST_Human | May, 2001 | 5 |
| EST_Mouse | May, 2001 | 5 |
| EST_Other | May, 2001 | 5 |
| aa_gadfly.dros.RELEASE2 | RELEASE2 | 6 |
| na_arms.dros.RELEASE2 | RELEASE2 | 6 |
| na_EST.dros | May, 2001 | 6 |
| nr_Arthropoda | Aug., 2001 | 7 |
| nr_Chordata | Aug., 2001 | 7 |
| Functional annotation | ||
| function.ontology | 2.99; Sep., 2001 | 8 |
| process.ontology | 2.88; Sep., 2001 | 8 |
| gene_association.fb | 1.29; Sep., 2001 | 8 |
1
University of Washington Genome Center; http://www.genome.washington.edu/UWGC
2
Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign; http://www.biotech.uiuc.edu/keck.htm
4
Organelle Genome Megasequencing Project, University of Montreal; http://megasun.bch.umontreal.ca/ogmpproj.html
5
National Center for Biotechnology Information (NCBI); http://www.ncbi.nim.nih.gov
6
Berkeley Drosophila Genome Project (BDGP); http://www.fruitfly.org
7
Sub-databases were extracted from nr using NCBI gene identification (gi) numbers for each taxonomic group.