Literature DB >> 10982889

An optimized protocol for analysis of EST sequences.

F Liang1, I Holt, G Pertea, S Karamycheva, S L Salzberg, J Quackenbush.   

Abstract

The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studies and an invaluable tool for the annotation of genomic sequences. We have developed a rigorous protocol for reconstructing the sequences of transcribed genes from EST and gene sequence fragments. A key element in developing this protocol has been the evaluation of a number of sequence assembly programs to determine which most faithfully reproduce transcript sequences from EST data. The TIGR Gene Indices constructed using this protocol for human, mouse, rat and a variety of other plant and animal models have demonstrated their utility in a variety of applications and are freely available to the scientific research community.

Entities:  

Mesh：

Year:  2000        PMID： 10982889      PMCID： PMC110731          DOI： 10.1093/nar/28.18.3657

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  17 in total

1.  CAP3: A DNA sequence assembly program.

Authors:  X Huang; A Madan
Journal:  Genome Res       Date:  1999-09       Impact factor: 9.043

2.  Comparison of gene indexing databases.

Authors:  J Bouck; W Yu; R Gibbs; K Worley
Journal:  Trends Genet       Date:  1999-04       Impact factor: 11.639

3.  ESTablishing a human transcript map.

Authors:  M S Boguski; G D Schuler
Journal:  Nat Genet       Date:  1995-08       Impact factor: 38.330

Review 4.  A gene map of the human genome.

Authors:  G D Schuler; M S Boguski; E A Stewart; L D Stein; G Gyapay; K Rice; R E White; P Rodriguez-Tomé; A Aggarwal; E Bajorek; S Bentolila; B B Birren; A Butler; A B Castle; N Chiannilkulchai; A Chu; C Clee; S Cowles; P J Day; T Dibling; N Drouot; I Dunham; S Duprat; C East; C Edwards; J B Fan; N Fang; C Fizames; C Garrett; L Green; D Hadley; M Harris; P Harrison; S Brady; A Hicks; E Holloway; L Hui; S Hussain; C Louis-Dit-Sully; J Ma; A MacGilvery; C Mader; A Maratukulam; T C Matise; K B McKusick; J Morissette; A Mungall; D Muselet; H C Nusbaum; D C Page; A Peck; S Perkins; M Piercy; F Qin; J Quackenbush; S Ranby; T Reif; S Rozen; C Sanders; X She; J Silva; D K Slonim; C Soderlund; W L Sun; P Tabar; T Thangarajah; N Vega-Czarny; D Vollrath; S Voyticky; T Wilmer; X Wu; M D Adams; C Auffray; N A Walter; R Brandon; A Dehejia; P N Goodfellow; R Houlgatte; J R Hudson; S E Ide; K R Iorio; W Y Lee; N Seki; T Nagase; K Ishikawa; N Nomura; C Phillips; M H Polymeropoulos; M Sandusky; K Schmitt; R Berry; K Swanson; R Torres; J C Venter; J M Sikela; J S Beckmann; J Weissenbach; R M Myers; D R Cox; M R James; D Bentley; P Deloukas; E S Lander; T J Hudson
Journal:  Science       Date:  1996-10-25       Impact factor: 47.728

5.  A quantitative comparison of DNA sequence assembly programs.

Authors:  M J Miller; J I Powell
Journal:  J Comput Biol       Date:  1994       Impact factor: 1.479

6.  A tool for analyzing and annotating genomic sequences.

Authors:  X Huang; M D Adams; H Zhou; A R Kerlavage
Journal:  Genomics       Date:  1997-11-15       Impact factor: 5.736

7.  Base-calling of automated sequencer traces using phred. II. Error probabilities.

Authors:  B Ewing; P Green
Journal:  Genome Res       Date:  1998-03       Impact factor: 9.043

8.  Sequence mapping by electronic PCR

Authors:  Gregory D Schuler
Journal:  Genome Res       Date:  1997-05       Impact factor: 9.043

9.  Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.

Authors:  M D Adams; A R Kerlavage; R D Fleischmann; R A Fuldner; C J Bult; N H Lee; E F Kirkness; K G Weinstock; J D Gocayne; O White
Journal:  Nature       Date:  1995-09-28       Impact factor: 49.962

10.  A physical map of 30,000 human genes.

Authors:  P Deloukas; G D Schuler; G Gyapay; E M Beasley; C Soderlund; P Rodriguez-Tomé; L Hui; T C Matise; K B McKusick; J S Beckmann; S Bentolila; M Bihoreau; B B Birren; J Browne; A Butler; A B Castle; N Chiannilkulchai; C Clee; P J Day; A Dehejia; T Dibling; N Drouot; S Duprat; C Fizames; S Fox; S Gelling; L Green; P Harrison; R Hocking; E Holloway; S Hunt; S Keil; P Lijnzaad; C Louis-Dit-Sully; J Ma; A Mendis; J Miller; J Morissette; D Muselet; H C Nusbaum; A Peck; S Rozen; D Simon; D K Slonim; R Staples; L D Stein; E A Stewart; M A Suchard; T Thangarajah; N Vega-Czarny; C Webber; X Wu; J Hudson; C Auffray; N Nomura; J M Sikela; M H Polymeropoulos; M R James; E S Lander; T J Hudson; R M Myers; D R Cox; J Weissenbach; M S Boguski; D R Bentley
Journal:  Science       Date:  1998-10-23       Impact factor: 47.728
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  41 in total

1.  A two-step strategy for constructing specifically self-subtracted cDNA libraries.

Authors:  Paolo Laveder; Cristiano De Pittà; Stefano Toppo; Giorgio Valle; Gerolamo Lanfranchi
Journal:  Nucleic Acids Res       Date:  2002-05-01       Impact factor: 16.971

2.  Gene expression in autumn leaves.

Authors:  Rupali Bhalerao; Johanna Keskitalo; Fredrik Sterky; Rikard Erlandsson; Harry Björkbacka; Simon Jonsson Birve; Jan Karlsson; Per Gardeström; Petter Gustafsson; Joakim Lundeberg; Stefan Jansson
Journal:  Plant Physiol       Date:  2003-02       Impact factor: 8.340

3.  Efficient clustering of large EST data sets on parallel computers.

Authors:  Anantharaman Kalyanaraman; Srinivas Aluru; Suresh Kothari; Volker Brendel
Journal:  Nucleic Acids Res       Date:  2003-06-01       Impact factor: 16.971

4.  ESTAnnotator: A tool for high throughput EST annotation.

Authors:  Agnes Hotz-Wagenblatt; Thomas Hankeln; Peter Ernst; Karl-Heinz Glatting; Erwin R Schmidt; Sándor Suhai
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

5.  PCAP: a whole-genome assembly program.

Authors:  Xiaoqiu Huang; Jianmin Wang; Srinivas Aluru; Shiaw-Pyng Yang; LaDeana Hillier
Journal:  Genome Res       Date:  2003-09       Impact factor: 9.043

6.  The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures.

Authors:  Yi Xing; Alissa Resch; Christopher Lee
Journal:  Genome Res       Date:  2004-02-12       Impact factor: 9.043

7.  Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes.

Authors:  Jena L Chojnowski; James Franklin; Yoshinao Katsu; Taisen Iguchi; Louis J Guillette; Rebecca T Kimball; Edward L Braun
Journal:  J Mol Evol       Date:  2007-08-03       Impact factor: 2.395

8.  Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species.

Authors:  Feng-Chi Chen; Sheng-Shun Wang; Shu-Miaw Chaw; Yao-Ting Huang; Trees-Juen Chuang
Journal:  Plant Physiol       Date:  2007-01-12       Impact factor: 8.340

9.  EST sequencing and time course microarray hybridizations identify more than 700 Medicago truncatula genes with developmental expression regulation in flowers and pods.

Authors:  Christian Firnhaber; Alfred Pühler; Helge Küster
Journal:  Planta       Date:  2005-06-21       Impact factor: 4.116

10.  SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read.

Authors:  Juan Falgueras; Antonio J Lara; Noé Fernández-Pozo; Francisco R Cantón; Guillermo Pérez-Trabado; M Gonzalo Claros
Journal:  BMC Bioinformatics       Date:  2010-01-20       Impact factor: 3.169
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