Literature DB >> 11910119

An automated annotation tool for genomic DNA sequences using GeneScan and BLAST.

A M Lynn1, C K Jain, K Kosalai, P Barman, N Thakur, H Batra, A Bhattacharya.   

Abstract

Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.

Mesh:

Year:  2001        PMID: 11910119     DOI: 10.1007/bf02811413

Source DB:  PubMed          Journal:  J Genet        ISSN: 0022-1333            Impact factor:   1.166


  20 in total

Review 1.  Genome data: what do we learn?

Authors:  W C Nierman; J A Eisen; R D Fleischmann; C M Fraser
Journal:  Curr Opin Struct Biol       Date:  2000-06       Impact factor: 6.809

Review 2.  Annotating eukaryote genomes.

Authors:  S Lewis; M Ashburner; M G Reese
Journal:  Curr Opin Struct Biol       Date:  2000-06       Impact factor: 6.809

3.  Genome annotation assessment in Drosophila melanogaster.

Authors:  M G Reese; G Hartzell; N L Harris; U Ohler; J F Abril; S E Lewis
Journal:  Genome Res       Date:  2000-04       Impact factor: 9.043

4.  Gene identification in bacterial and organellar genomes using GeneScan.

Authors:  R Ramakrishna; R Srinivasan
Journal:  Comput Chem       Date:  1999-03-30

5.  Recognition of protein coding regions in DNA sequences.

Authors:  J W Fickett
Journal:  Nucleic Acids Res       Date:  1982-09-11       Impact factor: 16.971

6.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

Authors:  R D Fleischmann; M D Adams; O White; R A Clayton; E F Kirkness; A R Kerlavage; C J Bult; J F Tomb; B A Dougherty; J M Merrick
Journal:  Science       Date:  1995-07-28       Impact factor: 47.728

Review 7.  Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors: 
Journal:  Science       Date:  1998-12-11       Impact factor: 47.728

8.  Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.

Authors:  R A Alm; L S Ling; D T Moir; B L King; E D Brown; P C Doig; D R Smith; B Noonan; B C Guild; B L deJonge; G Carmel; P J Tummino; A Caruso; M Uria-Nickelsen; D M Mills; C Ives; R Gibson; D Merberg; S D Mills; Q Jiang; D E Taylor; G F Vovis; T J Trust
Journal:  Nature       Date:  1999-01-14       Impact factor: 49.962

9.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

Authors:  S T Cole; R Brosch; J Parkhill; T Garnier; C Churcher; D Harris; S V Gordon; K Eiglmeier; S Gas; C E Barry; F Tekaia; K Badcock; D Basham; D Brown; T Chillingworth; R Connor; R Davies; K Devlin; T Feltwell; S Gentles; N Hamlin; S Holroyd; T Hornsby; K Jagels; A Krogh; J McLean; S Moule; L Murphy; K Oliver; J Osborne; M A Quail; M A Rajandream; J Rogers; S Rutter; K Seeger; J Skelton; R Squares; S Squares; J E Sulston; K Taylor; S Whitehead; B G Barrell
Journal:  Nature       Date:  1998-06-11       Impact factor: 49.962

10.  DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.

Authors:  J F Heidelberg; J A Eisen; W C Nelson; R A Clayton; M L Gwinn; R J Dodson; D H Haft; E K Hickey; J D Peterson; L Umayam; S R Gill; K E Nelson; T D Read; H Tettelin; D Richardson; M D Ermolaeva; J Vamathevan; S Bass; H Qin; I Dragoi; P Sellers; L McDonald; T Utterback; R D Fleishmann; W C Nierman; O White; S L Salzberg; H O Smith; R R Colwell; J J Mekalanos; J C Venter; C M Fraser
Journal:  Nature       Date:  2000-08-03       Impact factor: 49.962

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  4 in total

Review 1.  An introduction to the medicinal plant genome project.

Authors:  Shilin Chen; Li Xiang; Xu Guo; Qiushi Li
Journal:  Front Med       Date:  2011-06-22       Impact factor: 4.592

2.  An insight into the sialome of Anopheles funestus reveals an emerging pattern in anopheline salivary protein families.

Authors:  Eric Calvo; Adama Dao; Van M Pham; José M C Ribeiro
Journal:  Insect Biochem Mol Biol       Date:  2006-11-22       Impact factor: 4.714

3.  The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae.

Authors:  Guobin Zhang; Chunxia Ge; Pingping Xu; Shukai Wang; Senan Cheng; Yanbin Han; Yancui Wang; Yongbin Zhuang; Xinwei Hou; Ting Yu; Xitong Xu; Shuhan Deng; Quanquan Li; Yinqing Yang; Xiaoru Yin; Weidong Wang; Wenxue Liu; Chunxiao Zheng; Xuezhen Sun; Zhenlin Wang; Ray Ming; Shuting Dong; Jianxin Ma; Xiansheng Zhang; Cuixia Chen
Journal:  Nat Plants       Date:  2021-05-06       Impact factor: 15.793

4.  Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats.

Authors:  Vladimir Paar; Nenad Pavin; Ivan Basar; Marija Rosandić; Matko Gluncić; Nils Paar
Journal:  BMC Bioinformatics       Date:  2008-11-03       Impact factor: 3.169

  4 in total

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