Literature DB >> 11159316

MaskerAid: a performance enhancement to RepeatMasker.

J A Bedell1, I Korf, W Gish.   

Abstract

UNLABELLED: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid, a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting. AVAILABILITY: On request from the authors (see http://sapiens.wustl.edu/MaskerAid). CONTACT: maskeraid@watson.wustl.edu

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Mesh：

Year:  2000        PMID： 11159316     DOI： 10.1093/bioinformatics/16.11.1040

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  85 in total

1.  JSNP: a database of common gene variations in the Japanese population.

Authors:  Mika Hirakawa; Toshihiro Tanaka; Yoichi Hashimoto; Masako Kuroda; Toshihisa Takagi; Yusuke Nakamura
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

2.  Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.

Authors:  Paul M Harrison; Hedi Hegyi; Suganthi Balasubramanian; Nicholas M Luscombe; Paul Bertone; Nathaniel Echols; Ted Johnson; Mark Gerstein
Journal:  Genome Res       Date:  2002-02       Impact factor: 9.043

3.  Gene structure prediction and alternative splicing analysis using genomically aligned ESTs.

Authors:  Z Kan; E C Rouchka; W R Gish; D J States
Journal:  Genome Res       Date:  2001-05       Impact factor: 9.043

4.  Selecting for functional alternative splices in ESTs.

Authors:  Zhengyan Kan; David States; Warren Gish
Journal:  Genome Res       Date:  2002-12       Impact factor: 9.043

5.  Single nucleotide polymorphism mapping using genome-wide unique sequences.

Authors:  Leslie Y Y Chen; Szu-Hsien Lu; Edward S C Shih; Ming-Jing Hwang
Journal:  Genome Res       Date:  2002-07       Impact factor: 9.043

6.  EASED: Extended Alternatively Spliced EST Database.

Authors:  Heike Pospisil; Alexander Herrmann; Ralf H Bortfeldt; Jens G Reich
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

7.  Bipartite pattern discovery by entropy minimization-based multiple local alignment.

Authors:  Chengpeng Bi; Peter K Rogan
Journal:  Nucleic Acids Res       Date:  2004-09-23       Impact factor: 16.971

8.  De novo repeat classification and fragment assembly.

Authors:  Pavel A Pevzner; Paul A Pevzner; Haixu Tang; Glenn Tesler
Journal:  Genome Res       Date:  2004-09       Impact factor: 9.043

9.  Polymorphisms in the 3' UTR in the neurocalcin delta gene affect mRNA stability, and confer susceptibility to diabetic nephropathy.

Authors:  Masumi Kamiyama; Masaaki Kobayashi; Shin-ichi Araki; Aritoshi Iida; Tatsuhiko Tsunoda; Koichi Kawai; Masahito Imanishi; Makoto Nomura; Tetsuya Babazono; Yasuhiko Iwamoto; Atsunori Kashiwagi; Kohei Kaku; Ryuzou Kawamori; Daniel P K Ng; Torben Hansen; Peter Gaede; Oluf Pedersen; Yusuke Nakamura; Shiro Maeda
Journal:  Hum Genet       Date:  2007-08-02       Impact factor: 4.132

10.  HGVbase: a curated resource describing human DNA variation and phenotype relationships.

Authors:  D Fredman; G Munns; D Rios; F Sjöholm; M Siegfried; B Lenhard; H Lehväslaiho; A J Brookes
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971
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