title: MetWAMer: eukaryotic translation initiation site prediction.
abstract: BACKGROUND
  Translation initiation site (TIS) identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations.
  
  
  RESULTS
  MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage.
  
  
  CONCLUSIONS
  We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA. mespar1@iastate.edu
authors.forename: Michael E
authors.initials: ME
authors.lastname: Sparks
authors.forename: Volker
authors.initials: V
authors.lastname: Brendel
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D001499:Bayes Theorem; D018387:Codon, Initiator; D019295:Computational Biology; D005057:Eukaryotic Cells / Q000378:metabolism*; D008390:Markov Chains; D015233:Models, Statistical; D016366:Open Reading Frames; D011237:Predictive Value of Tests; D014176:Protein Biosynthesis; D011499:Protein Processing, Post-Translational; D012333:RNA, Messenger / Q000378:metabolism; D012372:ROC Curve; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D018387:Codon, Initiator; D012333:RNA, Messenger
references.citation: Bioinformatics. 2005 Mar 1;21(5):671-3
references.pmid: 15284102
references.citation: In Silico Biol. 2004;4(3):255-69
references.pmid: 15724279
references.citation: Bioinformatics. 2005 Sep 15;21(18):3596-603
references.pmid: 16076884
references.citation: Bioinformatics. 2005 Oct 15;21(20):3940-1
references.pmid: 16096348
references.citation: Bioinformatics. 2005 Nov 1;21 Suppl 3:iii20-30
references.pmid: 16306388
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61
references.pmid: 16381931
references.citation: BMC Bioinformatics. 2006;7:62
references.pmid: 16469098
references.citation: BMC Bioinformatics. 2006;7:121
references.pmid: 16526950
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W588-90
references.pmid: 16845076
references.citation: RNA. 2006 Oct;12(10):1893-906
references.pmid: 16921068
references.citation: Nat Rev Microbiol. 2007 Feb;5(2):128-40
references.pmid: 17224922
references.citation: Bioinformatics. 2007 Jul 1;23(13):i418-23
references.pmid: 17646326
references.citation: Bioinformatics. 2008 Mar 1;24(5):637-44
references.pmid: 18218656
references.citation: Nucleic Acids Res. 1999 Dec 1;27(23):4636-41
references.pmid: 10556321
references.citation: Proc Int Conf Intell Syst Mol Biol. 1999;:138-48
references.pmid: 10786296
references.citation: Bioinformatics. 2000 Sep;16(9):799-807
references.pmid: 11108702
references.citation: Bioinformatics. 2000 Nov;16(11):960-7
references.pmid: 11159307
references.citation: Bioinformatics. 2001 Aug;17(8):744-5
references.pmid: 11524378
references.citation: Bioinformatics. 2002 Feb;18(2):343-50
references.pmid: 11847092
references.citation: Nucleic Acids Res. 2002 Oct 1;30(19):4103-17
references.pmid: 12364589
references.citation: Yeast. 2003 Sep;20(12):1045-52
references.pmid: 12961752
references.citation: Bioinformatics. 2003 Oct;19 Suppl 2:ii103-12
references.pmid: 14534179
references.citation: Bioessays. 2003 Dec;25(12):1201-11
references.pmid: 14635255
references.citation: J Comput Biol. 2003;10(5):699-708
references.pmid: 14633394
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D354-9
references.pmid: 14681433
references.citation: Genome Res. 2004 Jan;14(1):142-8
references.pmid: 14707176
references.citation: BMC Bioinformatics. 2004 Feb 16;5:14
references.pmid: 15053846
references.citation: Bioinformatics. 2004 May 1;20(7):1157-69
references.pmid: 14764557
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: Bioinformatics. 2004 Jun 12;20(9):1453-4
references.pmid: 14871861
references.citation: Plant Physiol. 2004 Jun;135(2):745-55
references.pmid: 15173566
references.citation: Cell. 1978 Dec;15(4):1109-23
references.pmid: 215319
references.citation: Nucleic Acids Res. 1982 May 11;10(9):2997-3011
references.pmid: 7048259
references.citation: Nucleic Acids Res. 1987 Feb 25;15(4):1353-61
references.pmid: 3822832
references.citation: Nucleic Acids Res. 1987 Oct 26;15(20):8125-48
references.pmid: 3313277
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Nucleic Acids Res. 1990 Oct 25;18(20):6097-100
references.pmid: 2172928
references.citation: Mol Cell Biol. 1992 Oct;12(10):4796-805
references.pmid: 1406661
references.citation: Mamm Genome. 1996 Aug;7(8):563-74
references.pmid: 8679005
references.citation: Nucleic Acids Res. 1996 Sep 1;24(17):3439-52
references.pmid: 8811101
references.citation: Cell. 1997 Jun 13;89(6):831-8
references.pmid: 9200601
references.citation: Proc Int Conf Intell Syst Mol Biol. 1997;5:226-33
references.pmid: 9322041
references.citation: DNA Res. 1997 Jun 30;4(3):179-84
references.pmid: 9330905
references.citation: Nucleic Acids Res. 1998 Jan 15;26(2):544-8
references.pmid: 9421513
references.citation: Bioinformatics. 1998 Jun;14(5):384-90
references.pmid: 9682051
references.citation: Gene. 1999 Jul 8;234(2):187-208
references.pmid: 10395892
references.citation: J Comput Biol. 2005 Jul-Aug;12(6):702-18
references.pmid: 16108712