FGENESH-C - HMM plus similar cDNA-based gene structure prediction

Reference: Solovyev V.V. (2007) Statistical approaches in Eukaryotic gene prediction. In Handbook of Statistical genetics (eds. Balding D., Cannings C., Bishop M.), Wiley-Interscience; 3d edition, 1616 p.

HMM plus similar cDNA-based gene structure prediction (multiple genes, both chains)

Example

Paste nucleotide sequence here:
>>HUMSFRS_8213_DNA_14-FEB-1996 aagcgcagcggccgcatatataaacgcgaacccgggctcttcctcgtagt gccgccgggactcttggcgggtgaaggtgtgtgtcagcttttgcgtcact cgagccctgggcgctgcttgctaaagagccgagcacgcgggtctgtcatc atgtcgcgttacgggcggtacggaggaggtaagaagctggagtccggtga gggacgttggtgtgggtgtagtgagcactgcgaggccgtagggttgtcgc ggaggttgggagacggttattccgcgtgcgtaatggcggcttaggagcac gccagacgaagccggaggcagcggaggcggggtgctgaagggagacggga tggcgggtgtacatctctgccgagttccgtactcttgggcatttttgtgg cccaatccagcctaaagcagggttgagatgacggttttcgcgttgccttt ctcggagctgcccgccggcccccctccccccccgccctcggccggcggct gccattttgcgcacattgaggaccgtggtggcgcatttcctcagcgcttt cccgccacttcagcggacagatctggccgcagctgtaagatcgtggttgt gtttgagatagaacgaaattggcagctgtgagctgcatgttctcgtcaaa caatcggttaaattgcggaatgggaatggggacgtaatctgcgactggcg gctgggtttttttttagttatttccagcgcggtttatggctctggggcgg ggagctggagtcttgggcgagcctgtgcctgggacgtttgccgcggagga cgagagccggcgcagccctgctctcctggcccggcccctaccgaggccct cccgccgccgacgcgctgccgctgcgggcccgcgcgctcccggtgcgccc ggggctgccgggactcatgggtggggccgggccaggtcccgccccacgcc tcggtgtatcctaccacgcgtttctgcttgtgttcgggagggtcaccccg cattatttagaacgttaagaattttgtcaaaagtctagtttctcggggat ttgcggacttcaccagttttacgactaagttttgtcttggatagagggca ttaaatgtgctttacccaatcttgaggatggcccgttttaaggcaagtaa gtaattgaaacttgggccagattttgcataacgtgcattcttctatttgc gtttttaaacagaaaccaaggtgtatgttggtaacctgggaactggcgct ggcaaaggagagttagaaagggctttcagttattatggtcctttaagaac tgtatggattgcgagaaatcctccaggatttgcctttgtggaattcgaag atcctagagatgcagaagatgcagtacgaggactggatggaaagtaagta agatgttatgaatcttctgttcattaaaatatactgtggctagataatga acttagtgctaaatttggattctgaagtctggaagagaccttaaatagct ggtcatagtgttaaatgctaaaggcacacgaaggttaaagaagatagcgg agatggagttagggcttggtaaagaccgccaaagtttgttgggggggaag gagtggttggaaagagtgagtggttggaaagagttctttttaaatctata agtcctgaatatatttttaactttagaattttgttaatttgcttttatta gggtgatttgtggctcccgagtgagggttgaactatcgacaggcatgcct cggagatcacgttttgatagaccacctgcccgacgtccctttgatccaaa tgatagatgctatgagtgtggcgaaaagggacattatgcttatgattgtc atcgttacagccggcgaagaagaagcaggtatttattttaataaaggaat ggttggtattctagttaatcaagtaattcttttattagcaaggcagaaac tagtgtttttctataaacttgaatgttaattgtacaggtgtattttacaa tttgtgtttaattaaaaaaatgttactatattaataatcaacctggtcaa aacctttcaggtttcttcgtttgagtcagtcgccttgattcagaatgtca cgagccttatgatatcatgctgaggcgccttgcaaatccgacaattaaga tcctcctagaccttgaggtgatcagcataagaggccagatcccctcgagt catctacacctagcttcaccttattctttaaagggcagaaaatttgagac ggtgatcgccgtaacagtaaatttggcttacaattggggcccccctccgg tttagaaagaggaacaccagattgaccacattcccaactagaaaaatctt cttgcgtcaatcaagcctcacctggctcatttggctgtcagtttgatcgt cgttagattgaagaaaacatctagatgcagcgatcggctatagatacttc tagatcgtctagatctactagaccatgggccaaagagggtcgacctgcaa acttgcaaggtttatgttaaatacacattacagtgttttatattatgtaa tgctaagttgtaattcagcttttaacaaatctttttttaggtagtaaaaa aaaaaatactcaacaactaataggcccagagtttatttccaaatgagaca ctaaatttaaatagttttgagatttgatttcagcagaggcacacaaactc ttaaaaacgagttattgtctgacattttgttttttctctaacttgaaaaa taggtcacggtctagatcacattctcgatccagaggaaggcgatactctc gctcacgcagcaggagcaggggacgaaggtgagatcttgtttaactgaag tctttctgtattattattaaattcactggtagtccaacacagaaaaagct cattattttttttggagacagggtcttgctctgtcacccgggctggagta caggggcataaccacgactcactgctgccttgatgatctcttgggtttaa gcagttctcctacctcagcctcccgagtagctgggactgtaggcactgcc accatacccagctaatttttatttttgtagaaatggtcttgcactgtttc ccaggctggtctcaagctcctgggctcaaacgatcctcccgcagtgctgg gattatgggcatgagccactgcaccgttccccagttgaagtcttaacagg ccaaaaaaaaaaaaaactgtggagatggacttaaagttctttattttagg tcaaggtcagcatctcctcgacgatcaagatctatctctcttcgtagatc aagatcagcttcactcagaagatctaggtctggttctataaaaggatcga ggtatttccagtatgtaacactttttttccttacttgtgtttggattgtt cacatcttatcagtagagtgtcttaaggacataattcaaatggattgctt cagggaatatttgagatgtaaaagtttggaatttatgtgtaacttgtaac ataaatattaccctagtttcacagatgaagaaaagggctactagagattt taaggcttgttaggccgtgtggtagacaagggtcccaagcaatacagctc tactcaacactctgggtaggcatgttgctataaacttttctggcttcaga ttggatgatactagctctgaaagatggtaattgattttcccgacaaaaag gcctattagcaccaggaaaagagatcagaagcaagtagaaacatttctca tttttggaatgatggggttgatttgagacactggaaagttgactagggca gtagtgtgtacacagaaatgaatgtggattttttttttagaccgtttcag acctgaaaaaactaaagaaccagagctttactatttgtagaaggccttaa aaggagatagaatggaaaaaattgtaaaataagtattgcaacatgtaatt aacaatattgttatctgtaccaacgataaaaccgtggtacggaatgctac tgggagttaaattgctgtttaatagcacaaaacctttaaatgcaggaatt ctgaatcttgtggtctatttgagaaagctatgaaccatctctttagataa atttaaaagatagatatgtcagtctgatttggtttgtctgacagattgat ggctctcaaacataacttgatccgggaagaagcctgacaaatggggggcg gctttcttttcgtctggccttatcacctgaattagtctcagttcaggggt ctggttattttcatcctgccttagcctcctgagtagctgggactgccatt gtgtaccacagtgcccagctgagggatctgtgccttaagtgaggttagtt ttgcttccttcataccagtctcatcaaatgaaaaccatgtatttcccttg gatattacacagtgtttgagaatgttatacctgtacagaaactaaccaat tgagtgatagaaacaagtaattgaaatgggggttccttatgtctggtaac actttgtttgacagtgtgttagacagaataaggcaagtgttgcatcttgt ttagttttagcttctttatgcctgaccaacctaatacagtgttgagtagt taaggaaattcctttggactgattgatataattgtgttttttcacttttt ttattaagatccccgtcgaggtcaagatcaagatccaggtctatttcacg accaagaagcaggtagggtaaaaatttgattatccttttctagttatatg gcaccaatatccaaagagttcaaagtgtttttaattgttgaaattttaag tgttaactctaaacttaggttttagtgggaacacagtaccttatttgtgt atgtcctatttattactggctgactttccctgaacaagggaatgtaaaac tatagtgagaaagaagcttatgacttgggggattatattaaagaggccct tgttagaactgataggtgcatggagaagcatcctgaaatcgatgtgctta aagcagaatgtaaaagattaatcatgatgtagtaattgagtcattttttg aaaaacagttgttgaaagattggcttttgttagcaacaactggtaggatg tttttcagtttaagtgcagtctgacattttaagcttaggacatttggggg ttttacggtattggtgactacaagaaagggattggttagtactctttctt taatagaatttctcatgttttgacagccgatcaaagtccagatctccatc tccaaaaagaaggtaagctaaatgttttgttgccaaatcttgcctgtcaa gtgtggcctctgcagaatttgtttgcttactgctttgcagtctttgagct ctttggagaattggtgctatatagattaaaatactatgctaagtttctga aatactttttttttttgattcagtaacattagtttatacttttgctggaa atacttagtcataaaatgttagggtgattattaagatgtgattggtcctg tgagtacttggtagaaattttggtaagatagatgccttttccccacatgt acaatagatacaaagtgtggagaaaagtcttggaaatagttacctgccta gtgcttctttatgaccagaaaacttcaaatagttgtcatatttatctagt gcttcttaatgaccagaagacttcaaatagttgtcatatttaactgcagg ttgaccttgcaattttgacaaggaggatagcctaatttttttttttttct gggatggagttttcgctctgtccccaggcttggagtgcagtggctcaatc ttggctcactgcagcctccgattcccgggttcaagcaattatcctgtctc agcctcttgagcagttgggattacaggcacccaccgccaagcctggctaa ttttttgtatttctagtagagacggagtttcaccatgttggcgaggttgg tcttaaactcctgatcttaggtgatcacctgcctcggcctctcccaaagt gctggggttacaggcgtgagccaccgtgcctggccagggtagcctaatct taagccagggacaaaagatgaatatatgtaagtttcatgtcatttttagg tctttgctataggaaattagtaccttaggccacctttgaagttattgaaa gttagtacatgtacatgagagtttcaattgacactaattggatccaaacc taatgtttttctttttagtcgttccccatcaggaagtcctcgcagaagtg caagtcctgaaagaatggactgaagctctcaagttcaccctttagggaaa agttattttgtttacattattataagggatttgtgatgtctgtaaagtgt aacctaggaaagataattcaaccatctaatcaaaatggatctggattact atgtaaattcacagcagtaagga

Alternatively, load a local file with sequence in Fasta format:

Local file name:

Paste c-DNA sequence here:
>>HUMSFRS_8213_DNA_14-FEB-1996 cgagccctgggcgctgcttgctaaagagccgagcacgcgggtctgtcatc atgtcgcgttacgggcggtacggaggagaaaccaaggtgtatgttggtaa cctgggaactggcgctggcaaaggagagttagaaagggctttcagttatt atggtcctttaagaactgtatggattgcgagaaatcctccaggatttgcc tttgtggaattcgaagatcctagagatgcagaagatgcagtacgaggact ggatggaaaggtgatttgtggctcccgagtgagggttgaactatcgacag gcatgcctcggagatcacgttttgatagaccacctgcccgacgtcccttt gatccaaatgatagatgctatgagtgtggcgaaaagggacattatgctta tgattgtcatcgttacagccggcgaagaagaagcaggtcacggtctagat cacattctcgatccagaggaaggcgatactctcgctcacgcagcaggagc aggggacgaaggtcaaggtcagcatctcctcgacgatcaagatctatctc tcttcgtagatcaagatcagcttcactcagaagatctaggtctggttcta taaaaggatcgaggtatttccaatccccgtcgaggtcaagatcaagatcc aggtctatttcacgaccaagaagcagccgatcaaagtccagatctccatc tccaaaaagaagtcgttccccatcaggaagtcctcgcagaagtgcaagtc ctgaaagaatggactgaagctctcaagttcaccctttagggaaaagttat tttgtttacattattat

Alternatively, load a local file with sequence in Fasta format:

Local file name:

Select organism specific gene-finding parameters :
Total 353 genome-specific parameters are available for genefinders of FGENESH suite

Most gene finding parameters presented here were trained by Softberry for its own use and distribution, using proprietary and publicly available data. Some of the parameters were created for our academic customers, including Broad Institute/MIT, Washington University, University of Minnesota and The Institute for Genomic Research (TIGR).