|geneid documentation:||4. Running geneid|
|Table of contents:|
geneid input sequences must be in FASTA format:
FASTA sequence files show this structure:
Usually Fasta lines are 60 chars long but this is not mandatory.
To run geneid, type geneid [options] sequence_file where sequence_file is a FASTA formatted DNA sequence. Predictions are sent to the standard output. In addition, the program requires an organism specific parameters file (which can be broadly used within the phylogenetic group to which organism belongs. For instance, the human file may be used as well to predict genes in genomic sequences from vertebrates).The directory params contains several files for different organisms.
The parameters file may be speficied in three different ways:
|geneid command line options:|
|geneid output formats:|
geneid can process files containing more than one FASTA sequence. Moreover, external information as annotations and HSPs can be provided for every sequence. Requirement: records belonging to the same Locus must be sorted by first position.
Click over every example to see the corresponding output:
Enrique Blanco Garcia © 2003