View of /Sprout/Blocks.txt

We start with a set of closely-related genomes and form them into blocks. Every gene (i.e. feature) is wholly inside a block.

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
inside the block look the same or nearly the same.

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
all of the blocks that occupy that region.

SNP = single nucleotide polymorphism

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"Calling" genes means identifying the features in a genome.

If a genome is un-called:

     1. Call the tRNAs (A good package exists to do this.) tRNA = Transfer RNAs, which carry amino acids to glue them to proteins.
     2. Call the rRNAs (ribosomal RNAs). Only Gordon can do this.
     3. Call the other RNA types. Little is known about how to do this.
     4. Call PEGs (protein-encoding genes). Two tools called Glimmer and Critica, Bielefeld has a program that combines both.
     5. Fix the starts. Ralph Bulter is working on this.
     6. Map the IDs to the IDs in the previous version whenever possible.
     7. Reformat for SEED.

Genome data comes in via REFSEEK from the NCBI, Neils' Web Crawler, and EnSEmBL.