geneid docs

1. Prediction ab initio

## gff-version 2 ## date Thu Jul 5 11:05:29 2001 ## source-version: geneid v 1.1 -- geneid@imim.es ## Sequence cons.x8bisXs.970911 - Length = 151676 bps # Optimal Gene Structure. 7 genes. Score = 106.865317 # Gene 1 (Reverse). 11 exons. 618 aa. Score = 35.850634 cons.x8bisXs.970911 geneid_v1.1 Internal 4001 4150 0.31 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 4515 4905 2.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 5514 5750 1.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 7504 7569 1.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 7909 8116 7.21 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 8421 8506 1.30 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 9478 9592 5.78 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 9763 9955 0.18 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 10669 10770 1.74 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 10903 11070 7.45 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.1 First 11149 11284 6.41 - 0 gene_1 # Gene 2 (Reverse). 3 exons. 493 aa. Score = 25.252512 cons.x8bisXs.970911 geneid_v1.1 Terminal 21839 22922 18.37 - 1 gene_2 cons.x8bisXs.970911 geneid_v1.1 Internal 23679 24029 7.99 - 1 gene_2 cons.x8bisXs.970911 geneid_v1.1 First 30732 30775 -1.11 - 0 gene_2 # Gene 3 (Forward). 1 exons. 77 aa. Score = 1.009624 cons.x8bisXs.970911 geneid_v1.1 Single 31465 31695 1.01 + 0 gene_3 # Gene 4 (Reverse). 1 exons. 64 aa. Score = 0.612301 cons.x8bisXs.970911 geneid_v1.1 Single 48468 48659 0.61 - 0 gene_4 # Gene 5 (Forward). 6 exons. 220 aa. Score = 0.610088 cons.x8bisXs.970911 geneid_v1.1 First 53124 53261 0.33 + 0 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 87535 87599 -0.78 + 0 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 97769 97942 0.66 + 1 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 100189 100281 0.85 + 1 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 109098 109228 -1.00 + 1 gene_5 cons.x8bisXs.970911 geneid_v1.1 Terminal 112987 113045 0.55 + 2 gene_5 # Gene 6 (Reverse). 2 exons. 84 aa. Score = 1.237887 cons.x8bisXs.970911 geneid_v1.1 Terminal 113700 113816 -0.15 - 0 gene_6 cons.x8bisXs.970911 geneid_v1.1 First 114104 114238 1.38 - 0 gene_6 # Gene 7 (Forward). 6 exons. 365 aa. Score = 42.292270 cons.x8bisXs.970911 geneid_v1.1 First 135780 135891 2.76 + 0 gene_7 cons.x8bisXs.970911 geneid_v1.1 Internal 142150 142446 14.69 + 2 gene_7 cons.x8bisXs.970911 geneid_v1.1 Internal 144435 144603 5.04 + 2 gene_7 cons.x8bisXs.970911 geneid_v1.1 Internal 146071 146236 5.28 + 1 gene_7 cons.x8bisXs.970911 geneid_v1.1 Internal 147791 148030 12.98 + 0 gene_7 cons.x8bisXs.970911 geneid_v1.1 Terminal 150313 150423 1.53 + 0 gene_7

% geneid -G test.fasta

2. Introducing evidences (without group)

## Annotated gene cons.x8bisXs.970911 annotation Terminal 11190 11300 . - . cons.x8bisXs.970911 annotation Internal 21842 22922 . - . cons.x8bisXs.970911 annotation Internal 23679 24029 . - . cons.x8bisXs.970911 annotation Internal 30732 30772 . - . cons.x8bisXs.970911 annotation Internal 48471 48659 . - . cons.x8bisXs.970911 annotation First 52780 52800 . - .

## gff-version 2 ## date Thu Jul 5 11:27:58 2001 ## source-version: geneid v 1.1 -- geneid@imim.es ## Sequence cons.x8bisXs.970911 - Length = 151676 bps # Optimal Gene Structure. 5 genes. Score = 65.815047 # Gene 1 (Reverse). 9 exons. 453 aa. Score = 20.329739 cons.x8bisXs.970911 geneid_v1.1 Internal 4001 4150 0.31 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 4515 4905 2.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 5514 5750 1.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 7504 7569 1.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 7909 8116 7.21 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 8421 8506 1.30 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 9478 9592 5.78 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 9763 9827 -0.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 First 10071 10109 1.03 - 0 gene_1 # Gene 2 (Reverse). 2 exons. 60 aa. Score = 1.938525 cons.x8bisXs.970911 evidence Terminal 11190 11300 0.00 - 0 gene_2 cons.x8bisXs.970911 geneid_v1.1 First 11377 11445 1.94 - 0 gene_2 # Gene 3 (Reverse). 6 exons. 599 aa. Score = 0.016626 cons.x8bisXs.970911 geneid_v1.1 Terminal 13926 14039 0.02 - 0 gene_3 cons.x8bisXs.970911 evidence Internal 21842 22922 0.00 - 1 gene_3 cons.x8bisXs.970911 evidence Internal 23679 24029 0.00 - 1 gene_3 cons.x8bisXs.970911 evidence Internal 30732 30772 0.00 - 0 gene_3 cons.x8bisXs.970911 evidence Internal 48471 48659 0.00 - 0 gene_3 cons.x8bisXs.970911 evidence First 52780 52800 0.00 - 0 gene_3 # Gene 4 (Reverse). 2 exons. 84 aa. Score = 1.237887 cons.x8bisXs.970911 geneid_v1.1 Terminal 113700 113816 -0.15 - 0 gene_4 cons.x8bisXs.970911 geneid_v1.1 First 114104 114238 1.38 - 0 gene_4 # Gene 5 (Forward). 6 exons. 365 aa. Score = 42.292270 cons.x8bisXs.970911 geneid_v1.1 First 135780 135891 2.76 + 0 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 142150 142446 14.69 + 2 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 144435 144603 5.04 + 2 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 146071 146236 5.28 + 1 gene_5 cons.x8bisXs.970911 geneid_v1.1 Internal 147791 148030 12.98 + 0 gene_5 cons.x8bisXs.970911 geneid_v1.1 Terminal 150313 150423 1.53 + 0 gene_5

% geneid -GR evi.gff test.fasta

3. Introducing evidences (with group)

## Annotated gene cons.x8bisXs.970911 annotation Terminal 11190 11300 . - . id_x cons.x8bisXs.970911 annotation Internal 21842 22922 . - . id_x cons.x8bisXs.970911 annotation Internal 23679 24029 . - . id_x cons.x8bisXs.970911 annotation Internal 30732 30772 . - . id_x cons.x8bisXs.970911 annotation Internal 48471 48659 . - . id_x cons.x8bisXs.970911 annotation First 52780 52800 . - . id_x

## gff-version 2 ## date Thu Jul 5 11:28:29 2001 ## source-version: geneid v 1.1 -- geneid@imim.es ## Sequence cons.x8bisXs.970911 - Length = 151676 bps # Optimal Gene Structure. 4 genes. Score = 63.859896 # Gene 1 (Reverse). 9 exons. 453 aa. Score = 20.329739 cons.x8bisXs.970911 geneid_v1.1 Internal 4001 4150 0.31 - 2 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 4515 4905 2.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 5514 5750 1.36 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 7504 7569 1.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 7909 8116 7.21 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 8421 8506 1.30 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 9478 9592 5.78 - 1 gene_1 cons.x8bisXs.970911 geneid_v1.1 Internal 9763 9827 -0.77 - 0 gene_1 cons.x8bisXs.970911 geneid_v1.1 First 10071 10109 1.03 - 0 gene_1 # Gene 2 (Reverse). 6 exons. 598 aa. Score = 0.000000 cons.x8bisXs.970911 evidence Terminal 11190 11300 0.00 - 0 gene_2 cons.x8bisXs.970911 evidence Internal 21842 22922 0.00 - 1 gene_2 cons.x8bisXs.970911 evidence Internal 23679 24029 0.00 - 1 gene_2 cons.x8bisXs.970911 evidence Internal 30732 30772 0.00 - 0 gene_2 cons.x8bisXs.970911 evidence Internal 48471 48659 0.00 - 0 gene_2 cons.x8bisXs.970911 evidence First 52780 52800 0.00 - 0 gene_2 # Gene 3 (Reverse). 2 exons. 84 aa. Score = 1.237887 cons.x8bisXs.970911 geneid_v1.1 Terminal 113700 113816 -0.15 - 0 gene_3 cons.x8bisXs.970911 geneid_v1.1 First 114104 114238 1.38 - 0 gene_3 # Gene 4 (Forward). 6 exons. 365 aa. Score = 42.292270 cons.x8bisXs.970911 geneid_v1.1 First 135780 135891 2.76 + 0 gene_4 cons.x8bisXs.970911 geneid_v1.1 Internal 142150 142446 14.69 + 2 gene_4 cons.x8bisXs.970911 geneid_v1.1 Internal 144435 144603 5.04 + 2 gene_4 cons.x8bisXs.970911 geneid_v1.1 Internal 146071 146236 5.28 + 1 gene_4 cons.x8bisXs.970911 geneid_v1.1 Internal 147791 148030 12.98 + 0 gene_4 cons.x8bisXs.970911 geneid_v1.1 Terminal 150313 150423 1.53 + 0 gene_4

% geneid -GR evi.gff test.fasta