374
V. Mittard-Runte et al.
Korf I, Flicek P, Duan D et al (2001) Integrating genomic homology into gene structure prediction.
Bioinformatics 17(Suppl 1):S140–S148
Krause A, Ramakumar A, Bartels D et al (2006) Complete genome of the mutualistic, N2-fixing
grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 24(11):1385–1391
Krause L, McHardy AC, Nattkemper TW et al (2007) GISMO-gene identification using a support
vector machine for ORF classification. Nucleic Acids Res 35(2):540–549
Krogh A, Larsson B, von Heijne G et al (2001) Predicting transmembrane protein topology with a
hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580
Küster H, Becker A, Firnhaber C et al (2007) Development of bioinformatic tools to support ESTsequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
Phytochemistry 68(1):19–32
Lafay B, Lloyd AT, McLean MJ et al (1999) Proteome composition and codon usage in
spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res
27(7):1642–1649
Lagesen K, Hallin P, Rodland EA et al (2007) RNAmmer: consistent and rapid annotation of
ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108
Lander ES, Waterman MS (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2(3):231–239
Larsen TS, Krogh A (2003) EasyGene-a prokaryotic gene finder that ranks ORFs by statistical
significance. BMC Bioinformatics 4:21
Lawrence JG, Roth JR (1996) Selfish Operons: horizontal transfer may drive the evolution of gene
clusters. Genetics 143(4):1843–1860
Lee ML, Kuo FC, Whitmore GA et al (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl
Acad Sci U S A 97(18):9834–9839
Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index
computation and outlier detection. Proc Natl Acad Sci U S A 98(1):31–36
Li SS, Bigler J, Lampe JW et al (2005) FDR-controlling testing procedures and sample size
determination for microarrays. Stat Med 24(15):2267–2280
Lin M, Wei LJ, Sellers WR et al (2004) dChipSNP: significance curve and clustering of SNParray-based loss-of-heterozygosity data. Bioinformatics 20(8):1233–1240
Linke B, McHardy AC, Neuweger H et al (2006) REGANOR: a gene prediction server for
prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Appl
Bioinformatics 5(3):193–198
Liolios K, Mavromatis K, Tavernarakis N et al (2008) The genomes on line database (GOLD)
in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic
Acids Res 36:D475–D479
Lipshutz RJ, Fodor SP, Gingeras TR et al (1999) High density synthetic oligonucleotide arrays.
Nat Genet 21(1 Suppl):20–24
Lipshutz RJ, Morris D, Chee M et al (1995) Using oligonucleotide probe arrays to access genetic
diversity. Biotechniques 19(3):442–447
Liu JJ, Cutler G, Li W et al (2005) Multiclass cancer classification and biomarker discovery using
GA-based algorithms. Bioinformatics 21(11):2691–2697
Lomsadze A, Ter Hovhannisyan V, Chernoff YO et al (2005) Gene identification in novel
eukaryotic genomes by self-training algorithm. Nucleic Acids Res 33(20):6494–6506
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA
genes in genomic sequence. Nucleic Acids Res 25(5):955–964
Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic
Acids Res 26(4):1107–1115
Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab
initio eukaryotic gene-finders. Bioinformatics 20(16):2878–2879
Majoros WH, Pertea M, Salzberg SL (2005) Efficient implementation of a generalized pair hidden
Markov model for comparative gene finding. Bioinformatics 21(9):1782–1788
V. Mittard-Runte et al.
Korf I, Flicek P, Duan D et al (2001) Integrating genomic homology into gene structure prediction.
Bioinformatics 17(Suppl 1):S140–S148
Krause A, Ramakumar A, Bartels D et al (2006) Complete genome of the mutualistic, N2-fixing
grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 24(11):1385–1391
Krause L, McHardy AC, Nattkemper TW et al (2007) GISMO-gene identification using a support
vector machine for ORF classification. Nucleic Acids Res 35(2):540–549
Krogh A, Larsson B, von Heijne G et al (2001) Predicting transmembrane protein topology with a
hidden Markov model: application to complete genomes. J Mol Biol 305(3):567–580
Küster H, Becker A, Firnhaber C et al (2007) Development of bioinformatic tools to support ESTsequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
Phytochemistry 68(1):19–32
Lafay B, Lloyd AT, McLean MJ et al (1999) Proteome composition and codon usage in
spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res
27(7):1642–1649
Lagesen K, Hallin P, Rodland EA et al (2007) RNAmmer: consistent and rapid annotation of
ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108
Lander ES, Waterman MS (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2(3):231–239
Larsen TS, Krogh A (2003) EasyGene-a prokaryotic gene finder that ranks ORFs by statistical
significance. BMC Bioinformatics 4:21
Lawrence JG, Roth JR (1996) Selfish Operons: horizontal transfer may drive the evolution of gene
clusters. Genetics 143(4):1843–1860
Lee ML, Kuo FC, Whitmore GA et al (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl
Acad Sci U S A 97(18):9834–9839
Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: expression index
computation and outlier detection. Proc Natl Acad Sci U S A 98(1):31–36
Li SS, Bigler J, Lampe JW et al (2005) FDR-controlling testing procedures and sample size
determination for microarrays. Stat Med 24(15):2267–2280
Lin M, Wei LJ, Sellers WR et al (2004) dChipSNP: significance curve and clustering of SNParray-based loss-of-heterozygosity data. Bioinformatics 20(8):1233–1240
Linke B, McHardy AC, Neuweger H et al (2006) REGANOR: a gene prediction server for
prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Appl
Bioinformatics 5(3):193–198
Liolios K, Mavromatis K, Tavernarakis N et al (2008) The genomes on line database (GOLD)
in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic
Acids Res 36:D475–D479
Lipshutz RJ, Fodor SP, Gingeras TR et al (1999) High density synthetic oligonucleotide arrays.
Nat Genet 21(1 Suppl):20–24
Lipshutz RJ, Morris D, Chee M et al (1995) Using oligonucleotide probe arrays to access genetic
diversity. Biotechniques 19(3):442–447
Liu JJ, Cutler G, Li W et al (2005) Multiclass cancer classification and biomarker discovery using
GA-based algorithms. Bioinformatics 21(11):2691–2697
Lomsadze A, Ter Hovhannisyan V, Chernoff YO et al (2005) Gene identification in novel
eukaryotic genomes by self-training algorithm. Nucleic Acids Res 33(20):6494–6506
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA
genes in genomic sequence. Nucleic Acids Res 25(5):955–964
Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic
Acids Res 26(4):1107–1115
Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: two open source ab
initio eukaryotic gene-finders. Bioinformatics 20(16):2878–2879
Majoros WH, Pertea M, Salzberg SL (2005) Efficient implementation of a generalized pair hidden
Markov model for comparative gene finding. Bioinformatics 21(9):1782–1788