README.md

In derele/RbaseDB: SNP effects based on annotation

RbaseDB

SNP effects based on annotation

Genetic (DNA) sequence is annotated with effects of a change in each nucleotide base. This allows to query: what if at position X there would be a change to [A|G|C|T]?

Design

BASE ONTOLOGY

Concept by Mark Blaxter, Perl code by John Davey translated to R

by Emanuel Heitlinger:

• A: phase 1 any change is nonsynonymous
• B: phase 2 any change is nonsynonymous
• C: phase 3 any change is nonsynonymous
• D: phase 1 change to CT is nonsynonymous
• E: phase 2 change to CT is nonsynonymous
• F: phase 3 change to CT is nonsynonymous
• G: phase 1 change to AG is nonsynonymous
• H: phase 2 change to AG is nonsynonymous
• I: phase 3 change to AG is nonsense
• K: phase 1 change to GT is nonsynonymous
• L: phase 2 change to A is nonsense, to anything else is nonsynonymous
• J: phase 3 change to G is nonsynonymous
• M: phase 3 change to G is nonsense, to A is nonsynonymous
• N: phase 3 any change synonymous
• O: phase 1 change to T nonsense, others nonsynonymous
• P: phase 3 change to AG is nonsynonymous
• Q: phase 1 change to T nonsense, to G nonsynonymous
• R: phase 2 change to AG nonsense, others nonsynonymous
• S: phase 3 change to A nonsense, others nonsynonymous
• T: phase 3 change to A nonsense, G nonsynonymous

-W: all changes are unknown # EH added 08/23/2011

| | a | g | c | t |------|----------|------------|------------|---------- | a |aaa K OBF | aga R QBF | aca T ABN | ata I ABJ | |aag K OBF | agg R KBF | acg T ABN | atg M ABC | |aac N ABP | agc S ABP | acc T ABN | atc I ABJ | |aat N ABP | agt S ABP | act T ABN | att I ABJ | | | | | | g |gaa E OBF | gga G OBN | gca A ABN | gta V ABN | |gag E OBF | ggg G ABN | gcg A ABN | gtg V ABN | |gac D ABP | ggc G ABN | gcc A ABN | gtc V ABN | |gat D ABP | ggt G ABN | gct A ABN | gtt V ABN | | | | | | c |caa Q OBF | cga R QBN | cca P ABN | cta L GBN | |cag Q OBF | cgg R KBN | ccg P ABN | ctg L GBN | |cac H ABP | cgc R ABN | ccc P ABN | ctc L ABN | |cat H ABP | cgt R ABN | cct P ABN | ctt L ABN | | | | | | t |taa * AEF | tga * AEC | tca S ARN | tta L GRF | |tag * ABF | tgg W ALS | tcg S ALN | ttg L GLF | |tac Y ABI | tgc C ABT | tcc S ABN | ttc F ABP | |tat Y ABI | tgt C ABT | tct S ABN | ttt F ABP

derele/RbaseDB documentation built on Nov. 20, 2019, 12:03 a.m.