Published in Comput Appl Biosci on August 01, 1997
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
The Ensembl genome database project. Nucleic Acids Res (2002) 40.87
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GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
GeneWise and Genomewise. Genome Res (2004) 17.87
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
The Ensembl automatic gene annotation system. Genome Res (2004) 12.24
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Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73
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Frequent alternative splicing of human genes. Genome Res (1999) 6.68
Spidey: a tool for mRNA-to-genomic alignments. Genome Res (2001) 5.61
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Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol (2002) 4.90
An assessment of gene prediction accuracy in large DNA sequences. Genome Res (2000) 4.71
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res (2008) 4.38
ESTGenes: alternative splicing from ESTs in Ensembl. Genome Res (2004) 3.85
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature (2012) 3.53
Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res (2002) 3.12
Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res (2003) 3.03
Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping. Plant Physiol (2003) 2.50
The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol (2008) 2.43
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun (2014) 2.36
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol (2013) 2.28
GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res (2002) 2.20
Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene. Genome Res (2000) 2.19
Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries. Plant Physiol (2011) 2.04
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol (2006) 2.02
Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res (2004) 1.63
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol (2005) 1.58
Gene and alternative splicing annotation with AIR. Genome Res (2005) 1.55
Assessment of SAGE in transcript identification. Genome Res (2003) 1.52
Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti. Nucleic Acids Res (2012) 1.49
Approaches to Fungal Genome Annotation. Mycology (2011) 1.47
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics (2010) 1.41
Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. Genome Res (2004) 1.37
Isolation and functional expression of human COQ2, a gene encoding a polyprenyl transferase involved in the synthesis of CoQ. Biochem J (2004) 1.36
CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences. BMC Genomics (2012) 1.36
Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite. Genome Biol (2011) 1.36
Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles. Nucleic Acids Res (2005) 1.34
BeetleBase: the model organism database for Tribolium castaneum. Nucleic Acids Res (2006) 1.33
Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res (2003) 1.32
EbEST: an automated tool using expressed sequence tags to delineate gene structure. Genome Res (1998) 1.30
Gene prediction and verification in a compact genome with numerous small introns. Genome Res (2004) 1.30
The banana genome hub. Database (Oxford) (2013) 1.29
Using ESTs to improve the accuracy of de novo gene prediction. BMC Bioinformatics (2006) 1.24
Alfresco--a workbench for comparative genomic sequence analysis. Genome Res (2000) 1.19
Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation. Genome Res (2007) 1.14
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic Acids Res (2008) 1.13
Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). Brief Bioinform (2011) 1.12
Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res (2014) 1.11
The genomic sequence and comparative analysis of the rat major histocompatibility complex. Genome Res (2004) 1.11
ASEtrap: a biological method for speeding up the exploration of spliceomes. Genome Res (2006) 1.07
Sim4cc: a cross-species spliced alignment program. Nucleic Acids Res (2009) 1.05
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes. Front Plant Sci (2012) 1.04
Massive sequence comparisons as a help in annotating genomic sequences. Genome Res (2001) 0.99
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. Nucleic Acids Res (2004) 0.99
MutScreener: primer design tool for PCR-direct sequencing. Nucleic Acids Res (2006) 0.97
Nonobese diabetic congenic strain analysis of autoimmune diabetes reveals genetic complexity of the Idd18 locus and identifies Vav3 as a candidate gene. J Immunol (2010) 0.96
Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori. G3 (Bethesda) (2013) 0.95
The mouse Aire gene: comparative genomic sequencing, gene organization, and expression. Genome Res (1999) 0.94
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome. BMC Genomics (2009) 0.93
A cross-species alignment tool (CAT). BMC Bioinformatics (2007) 0.93
A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. Genome Res (2007) 0.92
Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection. Genome Res (2004) 0.91
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. Nucleic Acids Res (2012) 0.91
EAnnot: a genome annotation tool using experimental evidence. Genome Res (2004) 0.90
FELINES: a utility for extracting and examining EST-defined introns and exons. Nucleic Acids Res (2003) 0.90
Automatic generation of gene finders for eukaryotic species. BMC Bioinformatics (2006) 0.90
ACC2 is expressed at high levels in human white adipose and has an isoform with a novel N-terminus [corrected]. PLoS One (2009) 0.89
Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon. Genetics (2015) 0.87
The importance of identifying alternative splicing in vertebrate genome annotation. Database (Oxford) (2012) 0.87
galaxieEST: addressing EST identity through automated phylogenetic analysis. BMC Bioinformatics (2004) 0.87
Improvement of barley genome annotations by deciphering the Haruna Nijo genome. DNA Res (2015) 0.86
Sniffing out chemosensory genes from the Mediterranean fruit fly, Ceratitis capitata. PLoS One (2014) 0.86
RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA. Nucleic Acids Res (2014) 0.85
Sequencing and comparative analysis of the gorilla MHC genomic sequence. Database (Oxford) (2013) 0.85
Dynamic use of multiple parameter sets in sequence alignment. Nucleic Acids Res (2006) 0.84
Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes. Nucleic Acids Res (2003) 0.84
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics (2015) 0.84
Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Res (2012) 0.83
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. BMC Bioinformatics (2009) 0.82
Evaluation of genome sequencing quality in selected plant species using expressed sequence tags. PLoS One (2013) 0.82
Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinformatics (2012) 0.82
Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. Bioinformatics (2009) 0.81
DNannotator: Annotation software tool kit for regional genomic sequences. Nucleic Acids Res (2003) 0.81
Efficient plant gene identification based on interspecies mapping of full-length cDNAs. DNA Res (2010) 0.81
A method of precise mRNA/DNA homology-based gene structure prediction. BMC Bioinformatics (2005) 0.81
MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes. Evol Bioinform Online (2007) 0.79
A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism. BMC Genomics (2009) 0.79
bex-db: Bioinformatics workbench for comprehensive analysis of barley-expressed genes. Breed Sci (2013) 0.77
Visualizing sequence similarity of protein families. Genome Res (2004) 0.77
Molecular cloning of Plasmodium vivax calcium-dependent protein kinase 4. Korean J Parasitol (2010) 0.76
Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells. PLoS One (2016) 0.76
Ptpn22 and Cd2 Variations Are Associated with Altered Protein Expression and Susceptibility to Type 1 Diabetes in Nonobese Diabetic Mice. J Immunol (2015) 0.75
Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. BMC Genomics (2016) 0.75
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs. BMC Bioinformatics (2006) 0.75
Trace alignment and some of its applications. Bioinformatics (1998) 1.03