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Open AccessJournal ArticleDOI

‘DNA Strider’: a ‘C’ program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers

Christian Marck
- 11 Mar 1988 - 
- Vol. 16, Iss: 5, pp 1829-1836
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TLDR
DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers, designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work.
Abstract
DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot- codon adaptation index according to Sharp and Li. The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10,000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds.

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Citations
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Molecular cloning, nucleotide sequence, and occurrence of a 16.5-kilodalton outer membrane protein of Brucella abortus with similarity to pal lipoproteins.

TL;DR: It is demonstrated that Omp16 was expressed in the 34 Brucella strains tested, representing all six species and known biovars, and shows a remarkable degree of similarity to the sequences of three peptidoglycan-associated bacterial lipoproteins.
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Bacillopeptidase F of Bacillus subtilis: purification of the protein and cloning of the gene.

TL;DR: Characterization of this enzyme indicated that it was most likely the previously reported enzyme bacillopeptidase F. subtilis, and a "guess-mer" oligonucleotide hybridization probe was constructed on the basis of that sequence.
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Isolation and characterization of the gene encoding the surface membrane 3'-nucleotidase/nuclease of Leishmania donovani.

TL;DR: Results of Southern blot analyses were consistent with the 3'-NT/Nu being encoded by a single copy gene, and constitute the first report of the gene for this unique trypanosomatid surface membrane enzyme.
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Grapevine virus A: nucleotide sequence, genome organization, and relationship in the Trichovirus genus

TL;DR: The 5′ terminal region of the genomic RNA of grapevine virus A (GVA), a tentative member of the Trichovirus genus, was sequenced and evidence was obtained that the RNA is capped.
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A Second T-Region of the Soybean-Supervirulent Chrysopine-Type Ti Plasmid pTiChry5, and Construction of a Fully Disarmed vir Helper Plasmid

TL;DR: It is predicted that pKYRT1, a vir helper plasmid derived from pTiChry5, still contains all of TR and the leftmost 9 kb of TL, and demonstrated that p KYRT1 is not disarmed, and can transfer Ti plasmids DNA to plants.
References
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Journal ArticleDOI

A simple method for displaying the hydropathic character of a protein

TL;DR: A computer program that progressively evaluates the hydrophilicity and hydrophobicity of a protein along its amino acid sequence has been devised and its simplicity and its graphic nature make it a very useful tool for the evaluation of protein structures.
Journal ArticleDOI

Prediction of protein antigenic determinants from amino acid sequences.

TL;DR: The method was developed using 12 proteins for which extensive immunochemical analysis has been carried out and subsequently was used to predict antigenic determinants for the following proteins, finding that the prediction success rate depended on averaging group length.
Journal ArticleDOI

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

TL;DR: A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed, useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons ofCodon usage in different organisms.
Journal ArticleDOI

Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases.

TL;DR: The nucleotide sequence of two yeast RNA polymerase genes, RPO21 and RPO31, which encode the largest subunits of RNA polymerases II and III, respectively are determined.
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