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GeneMarkTM for MetaGenomes Analysis BETA | Heuristic 2009 | |||||||||||||
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Input Sequence(s) Title A title (an optional field) is used as the results header. For a sequence (either pasted in the box or loaded from a file) in FASTA format the ">" line is used as the title. Sequence Text Sequence text is accepted in single/multiple FASTA formats. Lines beginning with the symbol ">" are ignored. All numbers are ignored; rare characters other than T, C, A or G are replaced by C (to avoid the introduction of stop codons). Both upper and lower case letters are acceptable. Program Options Model Selection GeneMark.hmm gene prediction algorithm uses Hidden Markov models to represent genomic sequences. The 2008 heuristic models are an extension of 1999 models of a codon usage pattern common for a group of genomes with a given G-C content. (See Besemer & Borodovsky, PDF and program). We provide two types of models: 2008 Codon Polynomial order 3 (no temperature information is needed) 2008 Triplets with growth temperature (if some information about the growth temperature is available). Kingdom Mixture of bacteria and archaea should be used for all environmental samples as well as for human and other microbiomes. This option allows for using bacterial and archaeal heuristic models concurrently. This setting allows for achieving high sensitivity with somewhat lower specificity. Output Options Format GFF3 or "GeneMark.hmm" standard format. Nucleotide and amino acid sequences optional. Email address (required) The time of analysis depends on the sequence length. Once the job is finished the system will send you a notification email with a link to retrieve the results. |
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