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Revision Log
Revision 1.1.1.1 - (view) (download)
| 1 : | parrello | 1.1 | We start with a set of closely-related genomes and form them into blocks. Every gene (i.e. feature) is wholly inside a block. |
| 2 : | |||
| 3 : | A Genome can be thought of as a thread through blocks. A block contains one or more genome segments, one per thread in the block. All of the segments | ||
| 4 : | inside the block look the same or nearly the same. | ||
| 5 : | |||
| 6 : | Any region of the aligned genomes that is not contained within a single block is a major variation. The variation of the region is exposed by | ||
| 7 : | all of the blocks that occupy that region. | ||
| 8 : | |||
| 9 : | SNP = single nucleotide polymorphism | ||
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| 11 : | ------------------------------------------------------------------------------- | ||
| 12 : | |||
| 13 : | "Calling" genes means identifying the features in a genome. | ||
| 14 : | |||
| 15 : | If a genome is un-called: | ||
| 16 : | |||
| 17 : | 1. Call the tRNAs (A good package exists to do this.) tRNA = Transfer RNAs, which carry amino acids to glue them to proteins. | ||
| 18 : | 2. Call the rRNAs (ribosomal RNAs). Only Gordon can do this. | ||
| 19 : | 3. Call the other RNA types. Little is known about how to do this. | ||
| 20 : | 4. Call PEGs (protein-encoding genes). Two tools called Glimmer and Critica, Bielefeld has a program that combines both. | ||
| 21 : | 5. Fix the starts. Ralph Bulter is working on this. | ||
| 22 : | 6. Map the IDs to the IDs in the previous version whenever possible. | ||
| 23 : | 7. Reformat for SEED. | ||
| 24 : | |||
| 25 : | Genome data comes in via REFSEEK from the NCBI, Neils' Web Crawler, and EnSEmBL. |
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