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Theory:
• HMMgene is a program for prediction of genes in anonymous DNA. The program predicts whole genes, so the predicted exons always splice correctly. It can predict several whole or partial genes in one sequence, so it can be used on whole cosmids or even longer sequences. HMMgene can also be used to predict splice sites and start/stop codons. If some features of a sequence are known, such as hits to ESTs, proteins, or repeat elements, these regions can be locked as coding or non-coding and then the program will find the best gene structure under these constraints.
• The program is based on a hidden Markov model, which is a probabilistic model of the gene structure. This means that all predictions have associated probabilities that reflect how confident it is in the predictions. Apart from reporting the best prediction, HMMgene can also report the N best gene predictions for a sequence. This is useful if the there are several equally likely gene structures and may even indicate alternative splicing.
• HMMgene takes an input file with one or more DNA sequences in FASTA format. It also has a few options for changing the default behavior of the program.
• The output is a prediction of partial or complete genes in the sequences. The output is in a standardized format that is easily read by other programs, which specifies the location of all the predicted genes and their coding regions and scores for whole genes as well as exon scores.
• HMMgene only predicts coding regions. That is, the first exon (`firstex' below) is only the coding part of the first coding exon and similarly for the last exon (`lastex' below). Below a `gene' therefore means the region of the gene from start to stop codon.
SEQ1 HMMgene1.1 firstex 692 702 0.347 + 2 bestparse:cds_1
SEQ1 HMMgene1.1 exon_1 2473 2711 0.421 + 1 bestparse:cds_1
SEQ1 HMMgene1.1 exon_2 2897 3081 0.544 + 0 bestparse:cds_1
SEQ1 HMMgene1.1 exon_3 10376 10563 0.861 + 2 bestparse:cds_1
SEQ1 HMMgene1.1 exon_4 11841 11891 0.857 + 2 bestparse:cds_1
SEQ1 HMMgene1.1 exon_5 12387 12483 0.993 + 0 bestparse:cds_1
SEQ1 HMMgene1.1 exon_6 13076 13211 0.970 + 1 bestparse:cds_1
SEQ1 HMMgene1.1 exon_7 13332 13415 0.926 + 1 bestparse:cds_1
SEQ1 HMMgene1.1 exon_8 13515 13603 1.000 + 0 bestparse:cds_1
SEQ1 HMMgene1.1 exon_9 14180 14235 1.000 + 2 bestparse:cds_1
SEQ1 HMMgene1.1 exon_10 14321 14408 0.999 + 0 bestparse:cds_1
SEQ1 HMMgene1.1 exon_11 14483 14579 0.877 + 1 bestparse:cds_1
SEQ1 HMMgene1.1 exon_12 14697 14764 0.639 + 0 bestparse:cds_1
SEQ1 HMMgene1.1 exon_13 14901 15030 0.835 + 1 bestparse:cds_1
SEQ1 HMMgene1.1 lastex 15643 15704 0.987 + 0 bestparse:cds_1
SEQ1 HMMgene1.1 CDS 692 15704 0.132 + . bestparse:cds_1
Procedure:
• Retrieve the query nucleotide sequence in Fasta format from NCBI
(ncbi.nlm.nih.gov).
• Log in to http://cbs.dtu.dk/services/HMMgene/
• Paste the respective sequence in the given input box.
• Click the submit it sequence button
• As soon as the submit button is clicked the process continues for predicting the exons.
• Exons were predicted after complete execution of the program.