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Literature DB >> 9750195

A computer program for aligning a cDNA sequence with a genomic DNA sequence.

L Florea¹, G Hartzell, Z Zhang, G M Rubin, W Miller.

Abstract

We address the problem of efficiently aligning a transcribed and spliced DNA sequence with a genomic sequence containing that gene, allowing for introns in the genomic sequence and a relatively small number of sequencing errors. A freely available computer program, described herein, solves the problem for a 100-kb genomic sequence in a few seconds on a workstation.

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Substances：

Year: 1998 PMID： 9750195 PMCID： PMC310774 DOI： 10.1101/gr.8.9.967

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

25 in total

1. Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1.

Authors: T M Smith; M K Lee; C I Szabo; N Jerome; M McEuen; M Taylor; L Hood; M C King
Journal: Genome Res Date: 1996-11 Impact factor: 9.043

2. Discovering and understanding genes in human DNA sequence using GRAIL.

Authors: E C Uberbacher; Y Xu; R J Mural
Journal: Methods Enzymol Date: 1996 Impact factor: 1.600

3. PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation.

Authors: J Zhang; T L Madden
Journal: Genome Res Date: 1997-06 Impact factor: 9.043

4. The relationship between chromosome structure and function at a human telomeric region.

Authors: J Flint; K Thomas; G Micklem; H Raynham; K Clark; N A Doggett; A King; D R Higgs
Journal: Nat Genet Date: 1997-03 Impact factor: 38.330

5. A tool for aligning very similar DNA sequences.

Authors: K M Chao; J Zhang; J Ostell; W Miller
Journal: Comput Appl Biosci Date: 1997-02

6. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination.

Authors: M A Ansari-Lari; Y Shen; D M Muzny; W Lee; R A Gibbs
Journal: Genome Res Date: 1997-03 Impact factor: 9.043

7. A 1.1-Mb transcript map of the hereditary hemochromatosis locus.

Authors: D A Ruddy; G S Kronmal; V K Lee; G A Mintier; L Quintana; R Domingo; N C Meyer; A Irrinki; E E McClelland; A Fullan; F A Mapa; T Moore; W Thomas; D B Loeb; C Harmon; Z Tsuchihashi; R K Wolff; R C Schatzman; J N Feder
Journal: Genome Res Date: 1997-05 Impact factor: 9.043

8. Prediction of complete gene structures in human genomic DNA.

Authors: C Burge; S Karlin
Journal: J Mol Biol Date: 1997-04-25 Impact factor: 5.469

9. Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences.

Authors: W Makałowski; J Zhang; M S Boguski
Journal: Genome Res Date: 1996-09 Impact factor: 9.043

10. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains.

Authors: J C Oeltjen; T M Malley; D M Muzny; W Miller; R A Gibbs; J W Belmont
Journal: Genome Res Date: 1997-04 Impact factor: 9.043

309 in total

1. The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome.

Authors: J E Horvath; S Schwartz; E E Eichler
Journal: Genome Res Date: 2000-06 Impact factor: 9.043

2. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis.

Authors: J A Bailey; L Carrel; A Chakravarti; E E Eichler
Journal: Proc Natl Acad Sci U S A Date: 2000-06-06 Impact factor: 11.205

A computer program for aligning a cDNA sequence with a genomic DNA sequence.

1. Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1.

2. Discovering and understanding genes in human DNA sequence using GRAIL.

3. PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation.

4. The relationship between chromosome structure and function at a human telomeric region.

5. A tool for aligning very similar DNA sequences.

6. Large-scale sequencing in human chromosome 12p13: experimental and computational gene structure determination.

7. A 1.1-Mb transcript map of the hereditary hemochromatosis locus.

8. Prediction of complete gene structures in human genomic DNA.

9. Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences.

10. Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains.

1. The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome.

2. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis.

3. Massive sequence comparisons as a help in annotating genomic sequences.

4. HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project.

5. SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein.

6. DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.

7. BLAT--the BLAST-like alignment tool.

8. ViewGene: a graphical tool for polymorphism visualization and characterization.

9. Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling.

10. High-throughput variation detection and genotyping using microarrays.