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Annotation of /Sprout/Blocks.txt

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Revision 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
10 :    
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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