sgp2 is a program to predict genes by comparing anonymous genomic sequences from two different species. It combines tblastx, a sequence similarity search program, with geneid, an "ab initio" gene prediction program. Scores of exons are computed as log-likelihood ratios, function of the splice sites defining the exon, the coding bias in composition of the exon sequence as measured by a Markov Model of order five, and of the optimal alignment at the amino acid level between the target exon sequence and the counterpart homologous sequence in the reference set.

• Sequence 1 (Query)

 
Paste your FASTA sequence here
>HSCKBG GATCAGTTTTTTTTTTTAATCGCACTTATGCTTATTGTTTATTAGCGTTTCCTCCCATCT TTGCCTGAAGTCTCCGGGGACTGCCTTTGGGGGTCGGGTAAACTTGTCCCCTGCGAAGAG GGCCCAGGGTTGGGGTCTGGAAACTCCGAGGCTGCACTTGCCAGCGGCCTCTTAAGGCCA CAGCGTCCCCGTGGTTTCTGGCTCGCAGCCCCCCGAGACCCAGGACTTGTCCAAGGTCAG GGCACCGCGGGTGCCCCCGGGCTGGGCCGCAGCAGACTGCGCTTCCCGCGCGCCTTCGCT TTGCACCAGGATCGCCCAGGAAATGCCTGCGGGCACCTTGAGGAAGGTCGGCGGCTCCGG GCCAGCTCGCACTGGCCGGGGTGGGGCGGGGGCCGTACCTGCTGCGGAAGCCCCGAAAGC TTTCGCCCGGCCCCTCGCCGCCGCCGCGGGGGCTGGCTGGACTAGGCGGGCAGGCTCGAG GATGCGGATGAACCCAAGCGTCCTCGAGTGCCCGGAGGCTCTCCGCCTCAGTTTCCCGCC CAGAGGCAAGGGCGTGCGAGGGGATCCAGATATCCAAGGACCTGAGGTTTCGGCCTCGAG GTCTTGGGCGGGGGACTGGGCAGGCTGCGCGGGGTCCCAGCGAGGGGACAGCTCGGGTGG GCGGCCAGGGTGTTGGGGGCTGCGGGCGGCGGACAAAGCGGCGGCACCACCCCGCGGCGC GGGCCAATGGAATGAATGGGCTATAAATAGCCGCCAATGGGCGGCCCGCGTTGTGCCCCT TAAGAGCCGCGGGAGCGCGGAGCGGCCGCTGTTCGCCTGCGTCGCTCCGGGAGCTGCCGA CGGACGGAGCGCCCCCGCCCCCGCCCGGCCGCCCGGTGAGTGGGCCCGGGGGCCGGGGGC GTCCGCGCCCGGGCTAGGGGCGCTGCGAGCAAAGGGGGCGCGTCGCCTGGAGCGCGCGCC GGACCGGCCGGGGGTCCCCGGCGATGATGGCGCTCCCCGCGCGCGCTGCGGACCCCGCTG ACCTTGGCCGCGTCCCGGGGGGCGCCGGGGGGCCCGGCGGCGGGGGCCTGAGTGGTACGC GGGAGCCCGGGAACCCCGGCGTGCCGGTCCCCTCTGACCCCGCGTCTCCCCGCAGCCCGC CGCCGCCATGCCCTTCTCCAACAGCCACAACGCACTGAAGCTGCGCTTCCCGGCCGAGGA CGAGTTCCCCGACCTGAGCGCCCACAACAACCACATGGCCAAGGTGCTGACCCCCGAGCT GTACGCGGAGCTGCGCGCCAAGAGCACGCCGAGCGGCTTCACGCTGGACGACGTCATCCA GACAGGCGTGGACAACCCGGGTACGCGACCCCTCGGGGCCGGGGTCCCGGCCCCCCCTCC CCCCGCGCAGCCGCAGGGTCCTCAGCAGCGCGCTCGGGCCCGGCAGTGACGTCACTGTCC CCGTCCCGCGCCCCCTCCCCCAGGCCACCCGTACATCATGACCGTGGGCTGCGTGGCGGG CGACGAGGAGTCCTACGAAGTGTTCAAGGATCTCTTCGACCCCATCATCGAGGACCGGCA CGGCGGCTACAAGCCCAGCGATGAGCACAAGACCGACCTCAACCCCGACAACCTGCAGGT GCGGGGCTGCGGGCGGGCCGGGCGGGCGGGGCCGGGGTCTTCGGGCGCTCACTCCCGTCT CGCCTCCCAGGGCGGCGACGACCTGGACCCCAACTACGTGCTGAGCTCGCGGGTGCGCAC GGGCCGCAGCATCCGTGGCTTCTGCCTCCCCCCGCACTGCAGCCGCGGGGAGCGCCGAGC CATCGAGAAGCTCGCGGTGGAAGGTAGGGGCCGGGCGGGCCGAGGGGCGGCGGCGGCCGC GTCCCCCTCCCGGCGCGGTCCCCGCCCGCTTTTGTTTACGTCGCCCGGGAGCGGCAGCCG CCGTCGCGCTCTTATCTGCGCGCGCCCGGGTTCAGTTTCCCGGACCCACCGAGGGACGGA GGCCCAGCCCCCGCGCCCACAGCGGCCTGGGGCCCAGGGAGGGCGGGTCCTGGCGCGGGG TCACCGCCTGGGACCGTCGCCCGGGCCGTGAGGACTGGACGCCCGCAGATCCGGGCGGGT GGGGCCCTCTGACGTCCCCCGAGGTGGGGCACGGGGGCGGGCGGGTCCGCGCTGCGGGCT GGAGGGGCGGGCGCGGGAGCCCAGCGTCCTGAGCGCACCCCTCGCAGCCCTGTCCAGCCT GGACGGCGACCTGGCGGGCCGATACTACGCGCTCAAGAGCATGACGGAGGCGGAGCAGCA GCAGCTCATCGACGACCACTTCCTCTTCGACAAGCCCGTGTCGCCCCTGCTGCTGGCCTC GGGCATGGCCCGCGACTGGCCCGACGCCCGCGGTATCTGGTGCGTGTCCCTCTGCGCCCT CTCGCGGCGTCCTCCCTCCCCGCTACCTCCGCTTTCCCTCTCGCCCCCCTCGCGGGGGTG GGGCCCCTCGCGGCGAGGAGGAGGAGGAGGAGGAGGGAGGGGCCGGCCGCGCTCCGGGTC TGGGTTCCGTGCCGCGCCTCCTCCTGCGCCGGTGACCTTGGCCGAGCAGGTGCGTTAAGG GACTGGGCCCCGGCCCGTGGGGGCTCAGGACTCAGCAACACCTCCCCACCCCGAGACGTG AGGTGGGGGCGGGGCTCTCTGGCGCCTCTCCCCGACGGCCCTGGGAGCTGGAGCTCTTTG TTTTCTTTTCTCACTCCTCCGCCGCTGGGATTCTACCAGGGGCTGGTGACGCCAAAGCTT CTCCAGGGGCAGGGCTCCTACCCCCACTGTGGGGGGCGGGTCGGGCTGTCCTGGCGGTCC CTGGCCCCGCCCCACCTCGGGCCACAGCGCATGATGGCAGCTGGGGTTCTCCTGCTGTGA GGCGTCCCGGTTCCCCCGCCCGCCCCGTGTTGGCGGGTGGAGTCTTGGCAGCAGCCTCCA CTCCTGGGCATGGCAGGGAGCAGCACCTCAGGGACTTGGGAAGTTCCTTTGGTCTGGGGG CGGCCTGGGGCTTTTTTCTGGGTATGCCCTGAGACCAGCCCTCCCGCAGGCACAATGACA ATAAGACCTTCCTGGTGTGGGTCAACGAGGAGGACCACCTGCGGGTCATCTCCATGCAGA AGGGGGGCAACATGAAGGAGGTGTTCACCCGCTTCTGCACCGGCCTCACCCAGGTGCCAG GGACGGGGCAGGCCCAGACCCCAGGGCCCCAGCAGGGATGTGGGTGCCCCAGCATCAGTC CCCCCGGGGGATTTCCGGCACTGGGGAGTCTCAGGGCCTGTAGGGGTTTCAGGCAGGCCT TCTCCCTCATACCCTCTTCTCCGTCTGCAGATTGAAACTCTCTTCAAGTCTAAGGACTAT GAGTTCATGTGGAACCCTCACCTGGGCTACATCCTCACCTGCCCATCCAACCTGGGCACC GGGCTGCGGGCAGGTGTGCATATCAAGCTGCCCAACCTGGGCAAGCATGAGAAGTTCTCG GAGGTGCTTAAGCGGCTGCGACTTCAGAAGCGAGGCACAGGTGAGCAGGGCAGGTGCTGC GGCTTCCCGTGGCCTTTGGGCAGCCCTGTTTCCTCCGCCCTGACTTGCTGTCTCCCCAGG CGGTGTGGACACGGCTGCGGTGGGCGGGGTCTTCGACGTCTCCAACGCTGACCGCCTGGG CTTCTCAGAGGTGGAGCTGGTGCAGATGGTGGTGGACGGAGTGAAGCTGCTCATCGAGAT GGAACAGCGGCTGGAGCAGGGCCAGGCCATCGACGACCTCATGCCTGCCCAGAAATGAAG CCCGGCCCACACCCGACACCAGCCCTGCTGCTTCCTAACTTATTGCCTGGGCAGTGCCCA CCATGCACCCCTGATGTTCGCCGTCTGGCGAGCCCTTAGCCTTGCTGTAGAGACTTCCGT CACCCTTGGTAGAGTTTATTTTTTTGATGGCTAAGATACTGCTGATGCTGAAATAAACTA GGGTTTTGGCCTGCCTGCGTCTGAGTGGTGCCTCTCCTTTCCCAGGGGGGAGGGGGAAGG GCAGCAGCCAGGCCCCAGGAGTCTTGAGTCCTGGGCCTGCTGTGGGCCTCGCCTTCTGTG AGATGGGACAAGAGCCAGGAGGTGGCCACTCTGTTCTGCCTGCCCTACCTAGTCCATGGG CCCCTTCCCTCGTGTCTATCGGGCTGTGCAGGCAGGAACATGGGAGAGAGCGAGGGAGGA

... or search a FASTA file to process

• Sequence 2 (Subject)

 
Paste your FASTA sequence here
>MUSCRKNB CTGCAGCTGGACGTGGTGGCCCATGCCTTTAATCCCAGCACTTCGGAGGCAGAGGCAGGC GAATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTA TACAGAGAAACCCTGTCTTAAACAAACAAACAAACCAAAAAAGAAAAAAAGAAAGGGTGT GCCGCCACGCAGGACCTCACCTCTCTATTTGTATCAACTGCACCATCTACCACACTTTTC TACCCACGACCATTCCCTAATGAGCATCAGATCGAATCCAAACTTTCTCCCTCTACACGT TTCCTGATCTGTTTGTAGAGAAGGGACACCGTCTTTCTGTAGGCTGCATTCCATGAAGTG GGAATGCTAGGTCATAGAGCAATTTAAAAATTTTTTAACAAATACTGCCAAATTACTTTC CAGAAAAAGATGAAGCTGCTGGCAGCTGCAGCAGGCAAGGTGCGAACGCCTATCTTCACA CATTCCAATTCACACCTGGCACTGGCTGTGGTCAAATTCCAGGTTTCCCCTGTGTGTGTG TGTGGGGGGGGGGGTGGCACGGGGAGAGAGACTGTTTCAATGTGTTGGATCTGATTAATG AGCTTAATTTTGACTGGTGCTTCCTCCACCCCCAGTTTGCCTGCCGGTGTTGGGGAGTTC TTTGTGGGTGCGGTGGTAGAAACCGGTCCCCCGAGAAAAGGGACAGGAGATGAGAATTTG GAGATTCAAAAACAGTCTCTAGGAACTAAATGTCTTGAATCTTTCAGGGTCTGGGTCCAA GGGTCTTGGCGGTGTTCCTTAGAGCCCGCCCAAGGTCAGAACACCCTGGGTGCTTCCGGG CAGGACCTCAGCCAGACTGCGCCTCTGGTGTTGCACCAAGAACACCCAGGAGATGCCCGC AGGCACCTTGAGGAAGGTCGGCGGCTCTGTGGCTCTTGAGGATATGGCCTGGATGCGGTG TTTGGATGCTGTACCCAATGTTAAAAACCTGGACTCTCACCATGACCCTCTCTACAACGC AGTCGGCCTGAGGAGACAGGGAAGGCAGGAGCCTCAAGTGCCATCTGGCTTCCCAGACTC AGTTTCCTGCCCCCAGGCAGTGTGTGTGAAGCAGGTCTAGGATATCTATGGCTCTGGGGT TTCGTCTTAGGGATCCTGTGCGAGCACCACCGGGGTGGCCAAACTGCGCAGCGGGGTCGA GACTTGGGGACCGCTAGGGTGGGCCGCTGGGGGTGTCAAGGGCTGCTGCCTCGGACAAAG CGGCGGCACCACCCCAAAGCGCGGACCAATGGAATGAATGGGCTATAAATAGCCGCCAAT GGGAGGCCGCGACGCGCCCCTTAAGAGCTCAGGGAGCAGCGAGCAGCCGTCGTTCTTCTG CGCTGCGCCAGGAGCTGCAAGCACAGGCATCCATCGCCCCTGCTTCGTCCGGCATCCCGG TGAGCGGGTCCAAGGGCCAGGGGTATAGTCCTGCGGGGCTCTACGCTGTGGGGTGCGGGA CCGGGGCATCACGCCGAGCCTCGCTGCCGGGAGCGCTCATCGGACCCGCCCGGGAACTTG GGATGCGCTGGACTCTGACGATGCAGACCTCGCTGACCTTGGTGGCGTCCAGGGAAAGTC TCGGGGGTCCCAAGTGGTTTGCAGGTCCCTGGCGGCCGGTGTTTAAATCTCCTCTGACCC CGCTCTTCCCTGCAGCCCGCTGCCGCCGCCATGCCCTTCTCCAACAGCCATAATACGCAG AAGCTGCGCTTCCCGGCCGAGGATGAGTTCCCTGATCTGAGCAGCCACAACAACCATATG GCCAAGGTGCTGACCCCGGAGCTGTACGCCGAGCTCCGTGCCAAGTGCACGCCGAGCGGC TTTACTTTGGACGACGCCATTCAGACTGGCGTAGACAATCCGGGTATGCACACCCCTGTA GCGTCAGGCTTCCGCCTCCCCAAGAAGCCCCCCGGGCAAGGATCCCACTGCTCTTCCCTG AACCTTCGGTGGGCTGGGGTCCCCTGTTCCCCTCTCCGCGCTTAGCCTTAAGAGCCTCGG CTTGCTCCTGCCTGACGGTGACGTCACTGTCGCCGCGCCCCTCCTCCAGGCCACCCGTAC ATCATGACTGTGGGTGCAGTGGCGGGCGACGAGGAGAGTTACGACGTATTCAAGGACCTC TTCGACCCCATTATTGAGGAGCGGCACGGCGGCTACCAGCCCAGTGATGAGCACAAGACC GACCTCAACCCAGACAACCTGCAGGTGCGGGGAATCAGGGTCCGGGCGTGCTGGGGAGAG GGGTCTCGGCGCTCACTCTGGCCACCACCTTGTATTCCCAGGGTGGCGATGACCTGGACC CCAACTACGTGCTGAGCTCGCGAGTGCGCACAGGCCGCAGCATCCGCGGCTTCTGTCTCC CCCCGCACTGCAGCCGCGGGGAGCGCCGCGCCATCGAGAAGCTGGCAGTAGAAGGTAGGG GTCGGGTAACAGCCGCCAGAGCTGCTGCGCTCTTCTCTGCGCGCGCGTTCCCACTGGGGA CTGAGGTCGAAGACCCACCTTCGCCCGCGGGGACACACTGCTGCAGGCGGGGCGGCGGGC TTGCTCGCCCGCCCACCCTGTCCTTGAACTCTGCACTCCGCAGCTCTGTCCAGCCTAGAT GGCGACCTGTCTGGCAGGTACTACGCGCTCAAGAGCATGACTGAGGCGGAGCAGCAGCAG CTCATTGACGACCACTTCCTCTTCGATAAGCCTGTGTCGCCTCTGCTGCTGGCCTCCGGC ATGGCCCGCGACTGGCCGGATGCTCGTGGCATATGGTACGAGCCCTCTCCCCCCCCAGTC CCCAGAAGGTGGGGCCTGCCCTGAATTCCTAGTTTGTGCAGTGCCTCCCTCCGCCCAGGT GACCTTGGTTCTGCCGATGACTGTGGTCCTTGCGCTGCGGGAGGCCGCAGTCTCCAGGGA CTCAAGGGTGGTGACCAGTCTCTTTGGCGTCTGTTCTCCGCCCTCCTCCTGGGAGCCGGC GCTTCTTGTTTTCTCTCCACCTTCTCACCCCCTTATTCCGCCGGGATCGTGCCAGGTGCC AATGACGCAAAAGCCTCCGCACCGTCCGGGCAGGGCTCCTACCCCTGCAGACTGAGCGGG CGGAGGCGTGCTTCCTCTAGTGGGATGCTCTGGAGGCTCCAGACCCTTGCGGGCCACACA GCACATGACTGGTGATTGAGATGTATATGAGCTGCCTTCCTCCACTGTTGCTGGGATTGG CGTCTTGGTGACAGCTCACATTCCAGCACTTTGTTGAGGAAGCATTTTGTTTGAGGTCAC CCACCTATAGTGTCTTTCTTGGGTGTGATCTAAGGCCACATTCTGGCAGGGACTCCAGCC TGACTTTACCCCTCTTCTAGGCACAATGACAATAAGACTTTCCTGGTGTGGATTAACGAG GAGGACCACCTGCGAGTCATCTCCATGCAGAAGGGGGGCAACATGAAGGAAGTGTTCACC CGATTCTGCACCGGCCTCACTCAGGTCAGGCCTGGGCATTCCCCAGGGCTTCCTCACTAG GGGCGTTGGTGCTGGGGAGGGATCAGGGGCAGATCAGAGCCCACATCTCCCAGGGTCCGT AGGGCTTCCGGCCAGGCTTCCTTCTCTTAACTCTCCCTTCTCCACCTTCAGATCGAAACT CTCTTCAAGTCCAAGAACTATGAGTTCATGTGGAATCCTCACCTGGGCTACATCCTCACA TGCCCATCCAACCTGGGCACCGGACTGCGGGCAGGTGTACACATCAAGCTGCCCCACCTG GGGAAGCACGAGAAGTTCTCGGAGGTGCTCAAGCGGCTGCGGCTTCAGAAGCGAGGCACA GGTGAGGGGCAGAAGGCACAGGTGAGGGGCAGAAGGTGCAGGTGTTGTCCTCAGCCCCGC TGACCTGCCCATGTCCCACCGCAGGTGGCGTGGACACCGCTGCTGTCGGTGGGGTGTTTG ATGTCTCCAACGCTGACCGCCTGGGCTTCTCGGAGGTGGAACTGGTGCAGATGGTGGTGG ACGGAGTGAAACTACTCATTGAGATGGAGCAACGGCTCGAGCAGGGTCAGGCAATCGATG ACCTCATGCCGGCCCAGAAGTGAAGCCTGGCCCTCGCCACCATCAGGCTGCCGCTTCCTA ACTTATTACCCGGGCAGTGCCCGCCATGCATCCTTGATGTTTGCCGCCTGGCGCTGAGCC CTTAGCCTCGCTGTAGAGACTTCTGTCGCCCTGGGTAGAGTTTATTTTTTTGATGGCTAA GCTGTTGCTGACACTGAAAATAAACTAGGGTTTGGCCTGCCCTATGTCCGAGTGTTGCTT CTCCTTTCCTAGAGACAGTGTGTGTGTGTGTGTGTGTATGTGTGTGCGCGAGCTGGCCTT CTGTGTCATCTCACCTAGCAGATGAAACATGAGCCATAGAAGATACAGGGCAGAGAGGGA GGGAGGCTCTGAGTCCAGCCTTGAGCATCTAAGGACATCTGTGCTTGCAGGGTGGAGCCT TAGTGTTTCCTTAGTCCCAGC

... or search a FASTA file to process

Prediction Options

Organism: Homo sapiens vs Mus Musculus Drosophila melanogaster vs Anopheles Gambiae

Predicitions on: Sequence 1 (Query). Sequence 2 (Subject). Both sequences.

Output options

Output format:

geneid GFF geneid including CDS sequence geneid extended (only genes) GFF extended (only genes)

Do you want the tblastx output ?

Demo

To see a dummy example with the form ready to submit, click here.

This example contains the following features:

• geneid format
• Prediction on both sequences
• tblastx output
• Homo sapiens vs Mus Musculus

About sgp2 server

sgp2 ^server is the web server to sgp2, a program to predict genes, exons, splice sites and other signals along a DNA sequence. Visit sgp2 homepage for more information about this program.

Authors and acknowledgements

Version 1 of sgp2 has been mostly written by Gen�s Parra, Josep F. Abril and Roderic Guigo.
sgp2 ^server written by Enrique Blanco and Gen�s Parra with the always useful help of Moises Burset and Josep F. Abril.