1. Exercise 3 Inspecting the primary structure of a gene

2. Pevsner 2009

4. J Mol Biol 228, 1124--1136

5. Nature 409, 860-921

6. HMMgene Sequence identifier Program name Prediction (see table below for the meaning). Beginning End Score between 0 and 1 Strand: $+$ for direct and $-$ for complementary Frame (for exons it is the position of the donor in the frame) Group to which prediction belong. If several CDS's are found they will be called cds_1, cds_2, etc. `bestparse:' is there because alternative predictions will also be available

7. firstex The coding part of the first coding exon starting with the first base of the start codon. exon_NThe N'th predicted internal coding exon. lastex The coding part of the last coding exon ending with the last base of the stop codon. singleexThe coding part of an exon in a gene with only one coding exon. CDSCoding region composed of the exon predictions prior to this line. START Predicted start codon with position of first and last base (only with signal option). STOP Predicted stop codon with position of first and last base (only with signals option). DON Predicted donor site with position of the base before and after the splice site (only with signal option). ACC Predicted acceptor site with position of the base before and after the splice site (only signal option). HMMgene

8. Fgenesh G - predicted gene number, starting from start of sequence; Str - DNA strand (+ for direct or - for complementary); Feature - type of coding sequence: CDSf - First (Starting with Start codon), CDSi - internal (internal exon), CDSl - last coding segment, ending with stop codon); TSS - Position of transcription start (TATA-box position and score); Start and End - Position of the Feature; Score - Log likelihood*10 score for the feature; ORF - start/end positions where the first complete codon starts and the last codon ends.