Literature DB >> 8837029

The Staden sequence analysis package.

R Staden1.   

Abstract

I describe the current version of the sequence analysis package developed at the MRC Laboratory of Molecular Biology, which has come to be known as the "Staden Package." The package covers most of the standard sequence analysis tasks such as restriction site searching, translation, pattern searching, comparison, gene finding, and secondary structure prediction, and provides powerful tools for DNA sequence determination. Currently the programs are only available for computers running the UNIX operating system. Detailed information about the package is available from our WWW site: http:@www.mrc-lmb.cam.ac.uk/pubseq/.

Mesh:

Year:  1996        PMID: 8837029     DOI: 10.1007/bf02900361

Source DB:  PubMed          Journal:  Mol Biotechnol        ISSN: 1073-6085            Impact factor:   2.695


  28 in total

1.  Methods for discovering novel motifs in nucleic acid sequences.

Authors:  R Staden
Journal:  Comput Appl Biosci       Date:  1989-10

2.  Experiment files and their application during large-scale sequencing projects.

Authors:  J K Bonfield; R Staden
Journal:  DNA Seq       Date:  1996

3.  Methods for calculating the probabilities of finding patterns in sequences.

Authors:  R Staden
Journal:  Comput Appl Biosci       Date:  1989-04

4.  Identification of protein coding regions by database similarity search.

Authors:  W Gish; D J States
Journal:  Nat Genet       Date:  1993-03       Impact factor: 38.330

5.  Computer methods to locate signals in nucleic acid sequences.

Authors:  R Staden
Journal:  Nucleic Acids Res       Date:  1984-01-11       Impact factor: 16.971

6.  A computer program to enter DNA gel reading data into a computer.

Authors:  R Staden
Journal:  Nucleic Acids Res       Date:  1984-01-11       Impact factor: 16.971

7.  A simple method for displaying the hydropathic character of a protein.

Authors:  J Kyte; R F Doolittle
Journal:  J Mol Biol       Date:  1982-05-05       Impact factor: 5.469

8.  A new computer method for the storage and manipulation of DNA gel reading data.

Authors:  R Staden
Journal:  Nucleic Acids Res       Date:  1980-08-25       Impact factor: 16.971

9.  Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing.

Authors:  R Staden
Journal:  Nucleic Acids Res       Date:  1982-08-11       Impact factor: 16.971

10.  Recognition of protein coding regions in DNA sequences.

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

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  375 in total

1.  Multilocus sequence typing and antigen gene sequencing in the investigation of a meningococcal disease outbreak.

Authors:  I M Feavers; S J Gray; R Urwin; J E Russell; J A Bygraves; E B Kaczmarski; M C Maiden
Journal:  J Clin Microbiol       Date:  1999-12       Impact factor: 5.948

Review 2.  Design and implementation of an introductory course for computer applications in molecular genetics. A case study.

Authors:  S A Krawetz; D D Womble
Journal:  Mol Biotechnol       Date:  2001-01       Impact factor: 2.695

3.  The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti.

Authors:  T M Finan; S Weidner; K Wong; J Buhrmester; P Chain; F J Vorhölter; I Hernandez-Lucas; A Becker; A Cowie; J Gouzy; B Golding; A Pühler
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-31       Impact factor: 11.205

4.  The use of the nuclear protein-encoding gene, RNA polymerase II, for tick molecular systematics.

Authors:  Quentin Fang; James E Keirans; Tonya Mixson
Journal:  Exp Appl Acarol       Date:  2002       Impact factor: 2.132

5.  Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced.

Authors:  Pavel Neumann; Dana Pozárková; Jirí Macas
Journal:  Plant Mol Biol       Date:  2003-10       Impact factor: 4.076

6.  Unique mitochondrial genome architecture in unicellular relatives of animals.

Authors:  Gertraud Burger; Lise Forget; Yun Zhu; Michael W Gray; B Franz Lang
Journal:  Proc Natl Acad Sci U S A       Date:  2003-01-24       Impact factor: 11.205

7.  Genome-scale design of PCR primers and long oligomers for DNA microarrays.

Authors:  Stefan A Haas; Marc Hild; Anthony P H Wright; Torsten Hain; Driss Talibi; Martin Vingron
Journal:  Nucleic Acids Res       Date:  2003-10-01       Impact factor: 16.971

8.  Genome sequence of Lactobacillus helveticus, an organism distinguished by selective gene loss and insertion sequence element expansion.

Authors:  Michael Callanan; Pawel Kaleta; John O'Callaghan; Orla O'Sullivan; Kieran Jordan; Olivia McAuliffe; Amaia Sangrador-Vegas; Lydia Slattery; Gerald F Fitzgerald; Tom Beresford; R Paul Ross
Journal:  J Bacteriol       Date:  2007-11-09       Impact factor: 3.490

9.  Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement.

Authors:  Pavel Neumann; Andrea Koblízková; Alice Navrátilová; Jirí Macas
Journal:  Genetics       Date:  2006-04-03       Impact factor: 4.562

10.  Isolation and characterisation of the mating-type (MAT) locus from Rhynchosporium secalis.

Authors:  Simon J Foster; Bruce D L Fitt
Journal:  Curr Genet       Date:  2003-09-27       Impact factor: 3.886

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