
	Where results make sense

Topic: Gene finding

	Genome Biology \| Full text \| A comprehensive transcript index of the human genome generated using microarrays and ...
		These deficiencies are addressed in full-length gene cloning strategies [13], but cloning is still a laborious process which could be accelerated if we were able to start from a more accurate view of a putative gene [13].
		Figure 4c highlights tiling data under one condition for the beta-actin gene, a gene that is constitutively expressed in all tissues and often serves as a positive control in mRNA and protein expression experiments.
		An internal database of RNA genes and bacterial and vector sequences was aligned to the genome with BLASTN.
	www.genomebiology.com /2004/5/10/R73 (9545 words)

	Researchers locate Type II diabetes gene - Genetics - MSNBC.com (Site not responding. Last check: 2007-11-05)
		The discovery of the gene PTPN1 could lead to earlier treatment and new therapies, which already are being tested.
		One plan is to devise a drug that diminishes the gene's tendency to overproduce the blocking protein.
		The gene plays less of a role in the development of diabetes in fl adults, he said.
	www.msnbc.msn.com /id/6339987 (588 words)

	Genome Biology \| Full text \| An integrated gene annotation and transcriptional profiling approach towards the full gene ...
		After data processing and stringent filtering, we found 13,927 genes to be expressed during the Drosophila life-cycle, of which 10,378 genes belong to the BDGP predicted set and 3,497 are newly predicted in the Heidelberg Collection R1 (Table 2, Additional data file 3).
		The total number of genes in the new Heidelberg Collection R2 was 19,879 (Table 3, Additional data file 3), of which 6,224 are unique to the Heidelberg Prediction and 13,050 are common to both.
		A subset of genes was verified by in situ hybridization provided that our amplicon was in a size range from 150 bp to 1.5 kb and the gene showed expression during embryonic stages as measured by the microarray.
	www.genomebiology.com /2003/5/1/R3 (7818 words)

	GlimmerM User Manual
		The probabilities obtained with the decision trees are averaged to produce a smoothed estimate of the probability that the given subsequence is of a certain type.
		By surveying the public databases, one should be able to find all previously known genes of the target organism that are backed by laboratory evidence.
		One of the steps of the gene finding algorithm of GlimmerM is to determine potential splice sites in the DNA sequences presented at input.
	www.tigr.org /software/glimmerm/man.html (1655 words)

	BioMed Central \| Full text \| Gene finding in novel genomes
		Since sequence features such as codon bias [7] and splicing signals [8] vary from organism to organism, it is expected that gene finders may not perform optimally in a foreign genome.
		Genscan performs as well as recent gene finders designed specifically for Arabidopsis [16], was considered one of the standards for the Drosophila GASP experiments [3], and is one of the gene finders used by the International Rice Genome Sequencing Project [17].
		The GC content, proportion of single-exon genes, and average exon and intron lengths are all similar to the downloaded data for each genome (data not shown).
	www.biomedcentral.com /1471-2105/5/59 (3594 words)

	[No title]
		The results were especially good for the dataset containing sequences with several genes, where exon accuracy measures were improved by 30% compared to Genscan's results.
		Gene recognition by combination of several gene-finding programs.
		[4] Krogh, A. (1997) Two methods for improving performance of an HMM and their application for gene finding.
	www.cs.ubc.ca /~rogic/abstract3.html (385 words)

	BioMed Central \| Full text \| EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance
		Computational gene finding exploits the statistical differences in codon usage between coding and non-coding regions of DNA [4-6].
		In order to fully automate the construction of the gene finder, a data set of reliable genes was obtained through the following procedure, which is essentially the same as that used in [1].
		We believe the aim of a gene finding system is to help expert annotators as much as possible, and we consider the statistical significance of a gene an important help in classifying the predictions into almost certain genes and border-line genes needing more attention.
	www.biomedcentral.com /1471-2105/4/21 (7891 words)

	Gene-finding and Annotation
		Gene Prediction in Bacteria, Archaea, and in Eukaryotes
		I quote: "The "GeneMachine" is an integrated tool intended to perform both comparative and predictive gene identification techniques in a single run.
		The correct start codon of the Haemophilus influenzae dnaB gene: When DnaB proteins from various completed genome sequences are compared, the Haemophilus influenzae DnaB protein is considerably longer in the N-terminal than the other DnaB proteins, see: DnaB-dam.aln.
	virgil.ruc.dk /kurser/Sekvens/mngenefinding.htm (634 words)

	PAG-XII: (W154) USING ESTS FOR GENE IDENTIFICATION IN SOYBEAN: A HEURISTIC APPROACH (Site not responding. Last check: 2007-11-05)
		While gene numeration in completed genomes can be accomplished using a number of ab initio gene-finding algorithms, gene numeration and identification using EST data is far less straightforward.
		We will describe a heuristic algorithm for the identification and numeration of genes in the Williams and Williams82 cultivars of soybean which should be applicable for use in identifying actively transcribed genes in any highly inbred genome.
		Among the 1399 potential genes which could unambiguously be associated with their homologous transcript(s) in the non-Williams EST collection, approximately 1000 exhibited allelic variation.
	www.intl-pag.org /12/abstracts/W33_PAG12_154.html (237 words)

	Sequence of the Genome of Salmonella Bacteriophage P22 -- Byl and Kropinski 182 (22): 6472 -- The Journal of ...
		AGA and AGG, and that this influences expression of the gene (79).
		The isolation and sequence of missense and nonsense mutations in the cloned bacteriophage P22 tailspike protein gene.
		Transfer RNA genes and their significance to codon usage in the Pseudomonas aeruginosa lamboid bacteriophage D3.
	jb.asm.org /cgi/content/full/182/22/6472 (5456 words)

	PAG-IX: Sequence comparison between rice and Triticeae colinear regions as a tool for gene discovery and gene structure ... (Site not responding. Last check: 2007-11-05)
		The four genes are in the same orientation in rice, but the second gene is in inverted orientation in barley.
		General gene structure (exon number, size and location) was largely conserved between rice and barley and to a lesser extent with homologous genes in Arabidopsis.
		Colinearity of these four genes is not conserved in Arabidopsis compared to the two grass species.
	www.intl-pag.org /9/abstracts/W32_01.html (334 words)

	JS Online: Researchers Outline Lupus Gene Finding
		The researchers said that while problems with gene Ifi202 are specifically associated with lupus, many other subtle gene abnormalities are believed to be involved in the complex disorder.
		The research, published in the September issue of the journal Immunity, is confined to mice bred to be susceptible to the disease.
		The finding still needs to be duplicated by other labs and new studies must be conducted to see if the gene is found in humans with lupus.
	www.jsonline.com /alive/ap/sep01/ap-lupus-gene091801.asp (417 words)

	Integrating Database Homology in a Probabilistic Gene Structure Model (Site not responding. Last check: 2007-11-05)
		Probabilities are estimated for gene features by using dynamic programming to combine information from multiple sensors.
		We show how matches to homologous sequences from a database can be integrated into the probability estimation by interpreting the likelihood of a sequence in terms of the bit-cost to encode a sequence given a homology match.
		Experimental results in tests using a standard set of annotated genes showed that Genie identified 95% of coding nucleotides correctly with a specificity of 91%, and 77% of exons were identified exactly.
	www.fruitfly.org /~martinr/doc/genie-psb97-abstract.html (184 words)

	Dissecting the Genetic Architecture of Lipids, Lipoproteins, and Apolipoproteins : Lessons From Twin Studies -- Snieder ... (Site not responding. Last check: 2007-11-05)
		genes come to expression over this 10-year time span.
		lipoprotein lipase gene, and the macrophage scavenger receptor
		Heritability analysis of lipids and three gene loci in twins link the macrophage scavenger receptor to HDL cholesterol concentrations.
	atvb.ahajournals.org /cgi/content/full/19/12/2826 (5875 words)

	EuGene: an eukaryotic gene finder that combines several sources of evidence (ResearchIndex) (Site not responding. Last check: 2007-11-05)
		Abstract: In this paper, we describe the basis of EuG ene, a gene finder for eucaryotic organisms applied to Arabidopsis thaliana.
		The specificity of EuG ene, compared to existing gene finding software, is that EuG ene has been designed to combine the output of several information sources, including output of other software or user information.
		Gene Finding Integrating External Evidence - Thomas Schiex Catherine
	citeseer.ist.psu.edu /455195.html (497 words)

	PTEN Gene Finding May Lead to New Treatments for Prostate Cancer
		This finding will be especially relevant to metastatic prostate cancer if indeed the PTEN gene alters as the cancer progresses.
		Sawyers' work on the PTEN gene mutation and its relationship to the protein pathway sheds new light on prostate cancer, a disease that for years has frustrated scientists trying to target the killer of nearly 40,000 men every year.
		Clin Cancer Res 1998 Mar;4(3):811-5 Homozygous deletion of the PTEN tumor suppressor gene in a subset of prostate adenocarcinomas.
	www.psa-rising.com /medicalpike/gene_pten.htm (1028 words)

	KVL Bioinformatics, gene finding exercises
		The purpose of this exercise is to try different gene finding methods on a piece of provided DNA.
		Now try to find genes in the piece of DNA using different methods.
		>From the results of your search find the nucleotide positions of the starts and ends of the exons and write these into your table, then select ESTs covering as much as possible of your genomic DNA and try to reconstitute the entire gene (if this is possible).
	www.matfys.kvl.dk /bioinformatik/exercise-genefinding.html (700 words)

	Gene Finding and Expression
		Gene expression in both prokaryotes and eukaryotes is measured with massively parallel methods such as DNA microarrays.
		In collaboration with expert teams from industry and academia we design experiments to discover novel candidate genes for disease intervention and drug targets and unravel remaining mysteries in biology and medicine.
		The group is moving in the direction of a systems biology approach to interpretation of data in a network structure.
	www.cbs.dtu.dk /researchgroups/genefinding.php (477 words)

	Directory of open access journals
		Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition.
		It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation.
		RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.
	www.doaj.org /abstract?id=83807&toc=y (186 words)

	Gene finding (Site not responding. Last check: 2007-11-05)
		In the case of prokaryotes, this process is much easier due to the presence of specific promoter sequences as well as theabsence of splicing mechanisms.
		The rules can eitherbe a part of the DNA itself or enforced in the cellular environment by signals that are themselves derived by the translation ofthe DNA.
		A major problem in identifying genes in eukaryotes is the mechanism of splicing and often of multiple and overlappingsplice sites.
	www.therfcc.org /gene-finding-9190.html (306 words)

	Computational gene finding in prokaryotes (Site not responding. Last check: 2007-11-05)
		GENE PREDICTION in silico : Still a long way to go...
		Current methods of gene prediction, their strengths and weaknesses -- Mathé et a...
		Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccu...
	www.scienceoxygen.com /biology/473.html (254 words)

	Ion channel diseases -- Hübner and Jentsch 11 (20): 2435 -- Human Molecular Genetics
		gene may result in recessive or dominant disease.
		genes affect the ionic homeostasis of the inner ear.
		(1993) Mutations in the ryanodine receptor gene in central core disease and malignant hyperthermia.
	hmg.oupjournals.org /cgi/content/full/11/20/2435 (7129 words)

	SWBIC - Gene-Finding (Site not responding. Last check: 2007-11-05)
		It differs from the majority of existing gene finding algorithms in that it allows for partial as well as complete genes and for the occurrence of multiple genes in a single sequence, on either or both DNA strands.
		The program is based on a probabilistic model of gene structure/compositional properties and does not make use of protein sequence homology information.
		It is normally run as a post-processor to the Glimmer gene finder or to other prokaryotic gene finders.
	www.swbic.org /links/1.4.3.2.php (592 words)

	Finding prokaryotic genes by the frame-by-frame' algorithm: targeting gene starts and overlapping genes -- M.Shmatkov ...
		Finding prokaryotic genes by the frame-by-frame' algorithm: targeting gene starts and overlapping genes -- M.Shmatkov et al.
		Finding prokaryotic genes by the ‘frame-by-frame’ algorithm: targeting gene starts and overlapping genes
		It was shown that in terms of gene finding, the
	bioinformatics.oupjournals.org /cgi/content/abstract/15/11/874 (323 words)

	Identification and Analysis of Arabidopsis Expressed Sequence Tags Characteristic of Non-Coding RNAs -- MacIntosh et ...
		genes corresponding to 20,000 expressed sequence tag clones.
		Burleigh SM, Harrison MJ (1999) The down-regulation of Mt4-like genes by phosphate fertilization occurs systemically and involves phosphate translocation to the shoots.
		Lee JT, Davidow LS, Warshawsky D (1999) Tsix, a gene antisense to Xist at the X-inactivation center.
	www.plantphysiol.org /cgi/content/full/127/3/765 (6615 words)

	The VEIL gene finding system (Site not responding. Last check: 2007-11-05)
		We're in the midst of creating VEIL-2, which is trained on the vertebrate data and the human sequences collected by the Genie group.
		We then tested on a separate set of 114 vertebrate genes, We also have a human-only VEIL-2, which has been trained on 498 human sequences (single and multi-exon) and tested on a separate set of 121 non-homologous human sequences.
		GLIMMER is an interpolated Markov model system for finding genes in bacteria and archaea (with a eukaryotic version in development)`
	www.tigr.org /~salzberg/veil.html (957 words)

	Michael Q. Zhang's Lab: Computational Biology and Bioinformatics (Site not responding. Last check: 2007-11-05)
		The long-term goal of research in our lab is to use mathematical and statistical methods to identify functional elements in eucaryotic genomes, especially the genes and their control and regulatory elements.
		Since most of eukaryotic genes are split by intervening sequences (called introns), after transcription of a gene into a precursor mRNA, the introns have to be spliced out and the remaining fragments (called exons) have to be joined together as a mature mRNA before it can be translated into protein.
		Detecting cis regulatory elements and modeling gene expression networks are becoming new challenges in the functional genomics era.
	rulai.cshl.org (249 words)

	Martin's Corner
		for gene finding I have participated in the Drosophila jamboree to annotate the entire Drosophila melanogaster sequence.
		I have co-organized an experiment for an objective assessment of the state-of-the-art in genome annotation in genomic DNA using the 2.9 Mbases of the Adh region in Drosophila.
		These datasets were created for training and testing purposes of gene finding algorithms.
	www.fruitfly.org /reese (177 words)

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