Literature DB >> 6290988

A high speed, high capacity homology matrix: zooming through SV40 and polyoma.

J Pustell, F C Kafatos.   

Abstract

We present a new homology matrix program which owes its basic conception to the two-dimensional dot matrices previously described (1,2), but has important improvements and new features. It scores sequence homology over an adjustable range and plots the scores which are above an operator-determined filtration level. Its powerful noise-filtration system, capacity for compression without much loss of information, and speed of execution make this program a valuable tool in the analysis of homologies, internal direct repeats and reverse repeats, including palindromic sequences. The properties of the program are exemplified by analysis of SV40 and polyoma DNA sequences.

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Year:  1982        PMID： 6290988      PMCID： PMC321127          DOI： 10.1093/nar/10.15.4765

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


  10 in total

1.  Protein-DNA interactions at the origin of simian virus 40 DNA replication.

Authors:  R Tjian
Journal:  Cold Spring Harb Symp Quant Biol       Date:  1979

2.  The binding site on SV40 DNA for a T antigen-related protein.

Authors:  R Tjian
Journal:  Cell       Date:  1978-01       Impact factor: 41.582

3.  Computer analysis of nucleic acids and proteins.

Authors:  C L Queen; L J Korn
Journal:  Methods Enzymol       Date:  1980       Impact factor: 1.600

4.  The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes.

Authors:  D A Konkel; J V Maizel; P Leder
Journal:  Cell       Date:  1979-11       Impact factor: 41.582

5.  Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences.

Authors:  J Banerji; S Rusconi; W Schaffner
Journal:  Cell       Date:  1981-12       Impact factor: 41.582

6.  Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments.

Authors:  P A Hieter; E E Max; J G Seidman; J V Maizel; P Leder
Journal:  Cell       Date:  1980-11       Impact factor: 41.582

7.  Matrix program to analyze primary structure homology.

Authors:  J Novotny
Journal:  Nucleic Acids Res       Date:  1982-01-11       Impact factor: 16.971

8.  Enhanced graphic matrix analysis of nucleic acid and protein sequences.

Authors:  J V Maizel; R P Lenk
Journal:  Proc Natl Acad Sci U S A       Date:  1981-12       Impact factor: 11.205

9.  Coding potential and regulatory signals of the polyoma virus genome.

Authors:  E Soeda; J R Arrand; N Smolar; J E Walsh; B E Griffin
Journal:  Nature       Date:  1980-01-31       Impact factor: 49.962

10.  Three cDNA clones encoding mouse transplantation antigens: homology to immunoglobulin genes.

Authors:  M Steinmetz; J G Frelinger; D Fisher; T Hunkapiller; D Pereira; S M Weissman; H Uehara; S Nathenson; L Hood
Journal:  Cell       Date:  1981-04       Impact factor: 41.582
  10 in total
  87 in total

1.  Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium.

Authors:  Richard Sucgang; Guokai Chen; Wen Liu; Ryan Lindsay; Jing Lu; Donna Muzny; Gad Shaulsky; William Loomis; Richard Gibbs; Adam Kuspa
Journal:  Nucleic Acids Res       Date:  2003-05-01       Impact factor: 16.971

2.  The paternal gene of the DDK syndrome maps to the Schlafen gene cluster on mouse chromosome 11.

Authors:  Timothy A Bell; Elena de la Casa-Esperón; Heather E Doherty; Folami Ideraabdullah; Kuikwon Kim; Yunfei Wang; Leslie A Lange; Kirk Wilhemsen; Ethan M Lange; Carmen Sapienza; Fernando Pardo-Manuel de Villena
Journal:  Genetics       Date:  2005-09-19       Impact factor: 4.562

3.  On the evolution of the bacterial major sigma factors.

Authors:  P Szafrański
Journal:  J Mol Evol       Date:  1992-05       Impact factor: 2.395

4.  Reaction center and light-harvesting I genes from Rhodopseudomonas capsulata.

Authors:  D C Youvan; M Alberti; H Begusch; E J Bylina; J E Hearst
Journal:  Proc Natl Acad Sci U S A       Date:  1984-01       Impact factor: 11.205

5.  Software tools for analyzing pairwise alignments of long sequences.

Authors:  S Schwartz; W Miller; C M Yang; R C Hardison
Journal:  Nucleic Acids Res       Date:  1991-09-11       Impact factor: 16.971

6.  Four genes in two diverged subfamilies encode the ribulose-1,5-bisphosphate carboxylase small subunit polypeptides of Arabidopsis thaliana.

Authors:  E Krebbers; J Seurinck; L Herdies; A R Cashmore; M P Timko
Journal:  Plant Mol Biol       Date:  1988-11       Impact factor: 4.076

7.  DNA Binding and Sensor Specificity of FarR, a Novel TetR Family Regulator Required for Induction of the Fatty Acid Efflux Pump FarE in Staphylococcus aureus.

Authors:  Heba Alnaseri; Robert C Kuiack; Katherine A Ferguson; James E T Schneider; David E Heinrichs; Martin J McGavin
Journal:  J Bacteriol       Date:  2019-01-11       Impact factor: 3.490

8.  The intron boundaries and flanking rRNA coding sequences of Calliphora erythrocephala rDNA.

Authors:  V L Smith; K Beckingham
Journal:  Nucleic Acids Res       Date:  1984-02-10       Impact factor: 16.971

9.  Heptad motifs within the distal subdomain of the coiled-coil rod region of M protein from rheumatic fever and nephritis associated serotypes of group A streptococci are distinct from each other: nucleotide sequence of the M57 gene and relation of the deduced amino acid sequence to other M proteins.

Authors:  B N Manjula; K M Khandke; T Fairwell; W A Relf; K S Sriprakash
Journal:  J Protein Chem       Date:  1991-08

10.  Restriction fragment length polymorphism analysis of 16S ribosomal DNA of Streptococcus and Enterococcus species of bovine origin.

Authors:  B M Jayarao; J J Doré; S P Oliver
Journal:  J Clin Microbiol       Date:  1992-09       Impact factor: 5.948
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