An analysis of gene-finding programs for Neurospora crassa

Bioinformatics

Volumn 17, Issue 10, 2001, Pages 901-912

  Kraemer, Eileen ^a   Wang, Jian ^a,b   Guo, Jinhua ^a   Hopkins, Samuel ^a   Arnold, Jonathan ^b  

^a University of Georgia ^*  (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; EVALUATION; EXON; EXPERIMENT; GENE STRUCTURE; GENETIC ANALYSIS; MATHEMATICAL COMPUTING; METHODOLOGY; MOTIVATION; NEUROSPORA CRASSA; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAMETER; PREDICTION; PRIORITY JOURNAL; RELIABILITY; SENSITIVITY AND SPECIFICITY;

NEUROSPORA CRASSA;

EID: 0034771854     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.10.901     Document Type: Article

References (42)

1. Analysis of the pdx-1 (snz-1/sno-1) region of the Neurospora crassa genome: Correlation of pyridoxine-requiring phenotypes with mutations in two structural genes
2. The C.elegans gene unc-89, required for muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains
3. Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes
4. Statistical patterns in primary structures of functional regions in the E.coli genome: I. Oligonucleotide frequencies analysis
5. Statistical patterns in primary structures of functional regions in the E.coli genome: II. Non-homogeneous Markov models
6. Statistical patterns in primary structures of functional regions in the E.coli genome: III. Computer recognition of coding regions
7. GeneMark: Parallel gene recognition for both DNA strands
8. New genes in old sequences: A strategy for finding genes in a bacterial genome
9. Intrinsic and extrinsic approaches for detecting genes in a bacterial genome
10. Detection of new genes in the bacterial genome using Markov models for three gene classes
11. Regulatory sequences in the transcription of Neurospora crassa genes: CAAT box, TATA box, introns, poly (A) tail formation sequences
12. Regulatory sequences involved in the translation of Neurospora crassa mRNA: Kozak sequences and stop codons
13. Complete genome sequence of the methanogenic archaeon
14. Prediction of complete gene structures in human genomic DNA
15. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: Organizational symmetry around the origin of replication
16. Evaluation of gene structure prediction programs
17. Pombe: A gene-finding and exon-intron structure prediction system for fission yeast
18. A statistical analysis of sequence features within genes from Neurosora crassa
19. Base-calling of automated sequencer traces using Phred
20. Assessment of protein coding measures
21. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
22. The minimal gene complement of Mycoplasma genitalium
23. Identification of protein coding regions by database similarity search
24. Documentation for Phrap
25. The codon preference plot: Graphic analysis of protein coding sequences and prediction of gene expression
26. How to interpret an anonymous bacterial genome: Machine learning approach to gene identification
27. Deriving Ribosome Binding Site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction
28. Prediction of the coding regions in a contiguous 1 MB sequence of the genome of synechocystis sp. strain PCC6803
29. The Neurospora crassa genome. Cosmid libraries sorted by chromosome
30. Two methods for improving performance of an HMM and their application for gene finding
31. Evaluation of the exon predictions of the GRAIL software
32. GeneMark.hmm: New solutions for gene finding
33. Sequence analysis of the Neurospora crassa genome
34. Applications of GeneMark in multispecies environments
35. Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
36. Computer based exon detection: An evaluation metric for comparison
37. Identification of protein coding regions in genomic DNA
38. The C.elegans genome sequencing project: A beginning
39. HUGE: A database for human large proteins identified by Kazusa cDNA sequencing project
40. Metabolism and evolution of H.influenzae deduced from whole genome comparison to E.coli