TugasKu: Gene Prediction with softberry and GenScan

TUGAS BIOINFORMATIKA

GENE PREDICTION

 

Oleh

DIANA PUTRI HAPSARI

M0410018

JURUSAN BIOLOGI

FAKULTAS MATEMATIKA DAN ILMU PENGETAHUAN ALAM

UNIVERSITAS SEBELAS MARET

SURAKARTA

2012

Gene Prediction of Eucaryota

Nama gen: thymoma viral proto-oncogene 2, pseudogene

Nama spesies: Mus musculus

Accession number: NG_002439.4

Hasil Genscan:

  1.01 Init +    184    479       296    0    2    106    -31     317   0.195    18.26

 1.02 Term +    513   1632  1120    0    1    -15     53    1587   0.189   136.93

 1.03 PlyA +   1692   1697        6                                                           -0.45

 2.02 PlyA -   1730   1725          6                                                           1.05

 2.01 Term -   1880   1765      116    0    2     86     55      76     0.393     3.14

GenBank:

1 gaattcaagg ccaataccta aacatgataa aagcaatcta cagcaaacca gtagccaaca

61 tcaaagtaaa tggagagaag ctggaagcaa tcccactaaa atcagggact agacaaggct

121 gcccactttc tccctacctt ttcaacatag tacttgaagt attagccaga gcaattcgac

181 aacaaaagga gatcaagggg atacaaattg gaaaagagga agtcaaaata tcactttttg

241 cagatgatat gatagtatat ataagtgacc ctaaaaattc caacagagaa ctcctaaacc

301 tgataaacag cttcggtgaa gtagctggat ataaaattaa ctcaaacaag tcaatggcct

361 ttctctacac aaagaataaa caggctgaga aagaaattag ggaaacaaca cccttctcaa

421 tagccacaaa taatataaaa tatctcggcg tgactctaac gaaggaagtg aaagatctgt

481 atgataaaaa cttcaagtcc ctgaagaaag aaattaaaga agatctcaga agatggaaag

541 atctcccatg ctcatggatt ggcaggacca acattgtaaa aatggctatc ttgccaaaag

601 caatctacag attcaatgca atccccatta aaattccaac tcaattcttc aacgaattag

661 aaggagcaat ttgcaaattc atctggaata acaaaaaacc gaggatagca aaaactcttc

721 tcaaggataa aagaacctct ggtggaatca ccatgcctga cctaaagctt tactacagag

781 caattgtgat aaaaactgca tggtactggt atagagacag acaagtggac caatggaata

841 gaattgaaga cccagaaatg aacccacaca cctatggtca cttgatcttc gacaagggag

901 ccaaaaccat ccagtggaag aaagacagca ttttcaacaa ttggtgctgg cacaactggt

961 tgttatcatg tagaagaatg cgaatcgatc catacttatc tccttgtact aaggtcaaat

1021 ctaagtggat caaggaactt cacataaaac cagagacact gaaacttata gaggagaaag

1081 tggggaaaag ccttgaagat atgggcacag gggaaaaatt cctgaacaga acagcaatgg

1141 cttgtgctgt aagatcgaga attgacaaat gggacctaat gaaactccaa agtttctgca

1201 aggcaaaaga cactgtctat aagacaaaaa gaccaccaac agactgggaa aggatcttta

1261 cctatcctaa atcagatagg ggactaatat ccaacatata taaagaactc aagaaggtgg

1321 acctcagaaa atcaaataac ccccttaaaa aatggggctc agaactgaac aaagaattct

1381 cacctgagga ataccgaatg gcagagaagc acctgaaaaa atgttcaaca tccttaatca

1441 tcagggaaat gcaaatcaaa acaaccctga gattccacct cacaccagtg agaatggcta

1501 agatcaaaaa ttcaggtgac agcagatgct ggcgaggatg tggagaaaga ggaacactcc

1561 tccattgttg gtgggattgc aggcttgtac aaccactctg gaaatcagtc tggcggttcc

1621 tcagaaaatt ggacatagta ctaccggagg atccagcaat acctctcctg ggcatatatc

1681 cagaagatgc cccaactggt aagaaggaca catgctccac tatgttcata gcagccttat

1741 ttataatagc cagaaactgg gaagaaccca gatgcccctc aacagaggaa tggatacaga

1801 aaatgtggta catctacaca atggagtact actcagctat taaaaagaat gaatttatga

1861 aattcctagc caaatggatg gacctggaga gcatcatcct gagtgaggta acacaatcac

1921 aaaggaactc acacaatatg tactcactga taagtggata ctagcccaaa acctaggata

1981 cccacgatat aagatacaat ttcctaaaca catgaaactc aagaaaaatg aagactgaag

2041 tgtggacact atgcccctcc ttagaagtgg gaacaaaaca cccatggaag gagttacaga

2101 aacaaagtat ggagctgaga tgaaaggatg gaccatgtag agactgccat atccagtgat

2161 ccaccccata atcagcttcc aaatgctgac accattgcat acactagcaa gattttactg

2221 aaaggaccca gatgtagctg tctcttgtga gactatgccg gggcctagca aacacagaag

2281 tggatgctca cagtcagcta atggatggat cacagggctc ccaatggagg agctagagaa

2341 agtacccaag gagctaaagg gatcttcaac cctataggtg gaacaacatt atgaactaac

2401 cagtacccct gagctcttga ctctagctgc atatgtatca aaagatggcc tagtcggcca

2461 tcactggaaa gagaggccca ttggacacgc agactttgtg tgccccggta caggggaacg

2521 ccagggccaa agggggggag tgggtgggta ggggagtggg ggtgggtggg taagggggac

2581 ttttggtata gcattggaaa tgtaaatgag ctaaatacct aataaaaaat ggaaaaaaaa

2641 aaaaaaaaaa aaaagaaagg ccattgactt gtgtgagtta attttatatc cagctacttc

2701 attgaagctg tttatcaggc ttaggagttc tctggtggaa tttttagggt cacttatata

2761 tactatcata tcatctgcaa aaagtgatat tttgacttct tcctttccaa attgtatccc

2821 cttgatctcc ttttgttgtc taattgctct ggctaggacc tcaagtacaa tgttgaatag

2881 gtagggcgag agtggacagc cttgtctagt ccttgatttt agtgggattg cttccagctt

2941 ctcaccattt actttgatgt tggctattgg tttgctgtag attgctttta tcatgtttag

3001 gtatgggcct tgaattcctg atctttccaa gatttttatc atgaatgggt gttggatttt

3061 gtcaaatgct ttctc

//

Keterangan:

CDS                join (184.. 479, 513.. 1632, 1692.. 1697)

Gene                join (184.. 479, 513.. 1632, 1692.. 1697)

Exon                (480.. 512)

Gene Prediction of Procaryota

Nama gen: groEL

Nama spesies: Candidatus Blochmannia floridanus

Accession number: AY334447.1

GenBank:

1 tgannnnctt attnnnnnnn nnnnactgtg aaaattttta agggaaaatg aaatggcagc

61 taaagatgta aagtttggta atgatgctag agttaaaatg cttcgtggtg ttaacgtttt

121 agccgatgca gtgaaggtta ctttgggacc taaaggtcgg aatgttgttt tggataagtc

181 tttcggggct ccagtcatta caaaggatgg agtttcagtt gcacgtgaaa tcgaactaga

241 agataagttt gaaaatatgg gagctcagat ggtgaaagag gtggcttcta aggcaaatga

301 ttctgctggg gatggtacta caacggcaac tgtgttggct caatctatag ttaatgaagg

361 attgaaagct gtggctgctg gaatgaatcc tatggatttg aaacgtggta ttgataaagc

421 agtagtagca gcagtagagg agttaaaaaa attgtctgtt ccttgttcag atccaaaggc

481 tattgctcaa gtaggtacta tttctgcaaa ttccgatgaa acggtaggta aattgatagc

541 tcaagctatg gataaagttg gaaaagaggg agttattact gtagaagaag gatctggatt

601 gcaagatgag ttagatgttg ttgaaggtat gcagtttgat cgtggttatt tgtcccctta

661 ttttgttaat aagccagaaa gtggaactgt ggaattagaa catccattta ttttattggc

721 ggataaaaaa atatctaaca tcagggaaat gttacctata ttggaatctg tagctaaatc

781 tggaaaaccg ttacttatta ttgctgaaga tgtagaaggt gaagcgttgg ctactttggt

841 agtaaacaat atgcgtggaa tagtaaaggt tactgcagta aaggctccag gatttggtga

901 tcgtcgtaaa gctatgttgc aagatattgc gattttaacg tcaggaacag ttatttctga

961 agaaattgga ttagagttag aaaaagctac attggaagat atggggcaag ctaagagagt

1021 tttgattact aaagatgcta ctactattat tgatggtgtt ggtaataaat cctctataga

1081 tagtcgtgtg gctcaaatta atcagcaacg tgatgaagct acttcggatt atgatcgtga

1141 aaaacttcaa gaacgtgttg ctaaattagc tggtggggtt gcggtaataa aggttggtgc

1201 tgcaacagaa gttgaaatga aagaaaagaa agctcgtgtt gaagatgctc ttcatgctac

1261 cagagctgct gttgaagaag gtgttgtagc tggaggtggt gtggctttaa ttcgagtagc

1321 taatgctatt agaaatttgt gtggtgataa tgaagatcag aatgtaggta ttaaagtagc

1381 tagaagagct atggaagcgc ctttacgtca gattatggca aatgctggag aagaaccatc

1441 agtaattgct aataatgtac ggtcaggaga aggaaatact gggtataatg cagctactga

1501 aaaatatggt aacatgatag aattaggtat tttagatcca actaaagtta cnagatctgc

1561 tttgcagtat gcagct

//

Hasil Softberry:

Prediction of potential genes in microbial  genomes

 Time:   Tue Jan  1 00:00:00 2005

 Seq name: test sequence

 Length of sequence - 1576 bp

 Number of predicted genes - 1

 Number of transcription units - 1, operons - 0

     N    Tu/Op   Conserved  S       Start    End    Score   pairs(N/Pv)

     1     1 Tu  1     .       +    CDS    53 -    1574   2674

Predicted protein(s):

>GENE     1        53  -      1574   2674    507 aa, chain +

MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPVITKDGVSVAREI

ELEDKFENMGAQMVKEVASKANDSAGDGTTTATVLAQSIVNEGLKAVAAGMNPMDLKRGI

DKAVVAAVEELKKLSVPCSDPKAIAQVGTISANSDETVGKLIAQAMDKVGKEGVITVEEG

SGLQDELDVVEGMQFDRGYLSPYFVNKPESGTVELEHPFILLADKKISNIREMLPILESV

AKSGKPLLIIAEDVEGEALATLVVNNMRGIVKVTAVKAPGFGDRRKAMLQDIAILTSGTV

ISEEIGLELEKATLEDMGQAKRVLITKDATTIIDGVGNKSSIDSRVAQINQQRDEATSDY

DREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALI

RVANAIRNLCGDNEDQNVGIKVARRAMEAPLRQIMANAGEEPSVIANNVRSGEGNTGYNA

ATEKYGNMIELGILDPTKVTRSALQYA

Keterangan:

CDS                join(53..1574)

                        /product= “heat shock protein”

Gene                join(53..1574)