Glimmer ICM builder(构建interpolated context model (

功能简介

分析模块,输入基因集数据,构建interpolated context model (ICM),该训练模型结果,在Glimmer3中,能够用于后续的基因预测。


示例

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)


分析模块引用了 glimmer v3.02b 软件(https://ccb.jhu.edu/software/glimmer/)。

相关文献如下所示:

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).