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Glimmer ICM builder (version 0.2)

Trainings Dataset:

A set of known genes in FASTA format.

Set the depth of the ICM:

The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position.

Set the period of the ICM:

The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ...

Set the width of the ICM:

The width includes the predicted position.

Do not use any input strings with in-frame stop codons:

Specify start codons as:

Use Genbank translation table to specify stop codons:

What it does

This program constructs an interpolated context model (ICM) from an input set of sequences.

This model can be used by Glimmer3 to predict genes.

TIP To extract CDS from a GenBank file use the tool Extract ORF from a GenBank file.

Example

Input:

- Genome Sequence

        >CELF22B7  C.aenorhabditis elegans (Bristol N2) cosmid F22B7
        GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
        GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
        TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
        TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
        GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
        ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
        AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
        CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
        TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
        AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
        GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
        AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
        CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
        AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
        GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
        .....

Output::: interpolated context model (ICM)

References

A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).