‘DNA Strider’: a ‘C’ program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers
TL;DR: 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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TL;DR: Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin- 4 regulates lin- 14 translation via an antisense RNA-RNA interaction.
11,932 citations
TL;DR: Human monocytes induced with adherent IgG secrete an interleukin-1 receptor antagonist which could be important for the in vivo regulation of IL-1 activity and analysis of monocyte RNA indicates that the gene is transcriptionally regulated.
Abstract: Human monocytes induced with adherent IgG secrete an interleukin-1 receptor antagonist which could be important for the in vivo regulation of IL-1 activity. A complementary DNA for this molecule has been isolated from a human monocyte library. Analysis of monocyte RNA indicates that the gene is transcriptionally regulated. The sequence of the receptor antagonist indicates that it is structurally similar to IL-1 beta. Expression of the cDNA in Escherichia coli yields IL-1 receptor antagonist activity.
1,115 citations
TL;DR: The molecular cloning and characterization of several related cDNAs from which can be deduced the full-length p68 kinase sequence are reported, which predicts a protein of 550 amino acids containing all of the conserved domains specific for members of the protein kinase family.
973 citations
TL;DR: The results suggest that hydrophobins may have a role in the elaboration of infective structures by fungi and may fulfill other functions in fungal phytopathogenesis.
Abstract: Differential cDNA cloning was used to identify genes expressed during infectious growth of the fungal pathogen Magnaporthe grisea in its host, the rice plant. We characterized one of these genes, MPG1, in detail. Using a novel assay to determine the proportion of fungal biomass present in the plant, we determined that the MPG1 transcript was 60-fold more abundant during growth in the plant than in culture. Mpg1 mutants have a reduced ability to cause disease symptoms that appears to result from an impaired ability to undergo appressorium formation. MPG1 mRNA was highly abundant very early in plant infection concomitant with appressorium formation and was also abundant at the time of symptom development. The MPG1 mRNA was also expressed during conidiation and in mycelial cultures starved for nitrogen or carbon. MPG1 potentially encodes a small, secreted, cysteine-rich, moderately hydrophobic protein with the characteristics of a fungal hydrophobin. Consistent with the role of the MPG1 gene product as a hydrophobin, Mpg1 mutants show an "easily wettable" phenotype. Our results suggest that hydrophobins may have a role in the elaboration of infective structures by fungi and may fulfill other functions in fungal phytopathogenesis.
852 citations
TL;DR: A gene has now been isolated from the critical region on Xp22.3 to which Kallmann's syndrome locus has been assigned: this gene escapes X inactivation, has a homologue on the Y chromosome, and shows an unusual pattern of conservation across species.
Abstract: Kallmann's syndrome (clinically characterized by hypogonadotropic hypogonadism and inability to smell) is caused by a defect in the migration of olfactory neurons, and neurons producing hypothalamic gonadotropin-releasing hormone. A gene has now been isolated from the critical region on Xp22.3 to which the syndrome locus has been assigned: this gene escapes X inactivation, has a homologue on the Y chromosome, and shows an unusual pattern of conservation across species. The predicted protein has significant similarities with proteins involved in neural cell adhesion and axonal pathfinding, as well as with protein kinases and phosphatases, which suggests that this gene could have a specific role in neuronal migration.
794 citations
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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.
21,921 citations
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.
Abstract: A method is presented for locating protein antigenic determinants by analyzing amino acid sequences in order to find the point of greatest local hydrophilicity. This is accomplished by assigning each amino acid a numerical value (hydrophilicity value) and then repetitively averaging these values along the peptide chain. The point of highest local average hydrophilicity is invariably located in, or immediately adjacent to, an antigenic determinant. It was found that the prediction success rate depended on averaging group length, with hexapeptide averages yielding optimal results. 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: hepatitis B surface antigen, influenza hemagglutinins, fowl plague virus hemagglutinin, human histocompatibility antigen HLA-B7, human interferons, Escherichia coli and cholera enterotoxins, ragweed allergens Ra3 and Ra5, and streptococcal M protein. The hepatitis B surface antigen sequence was synthesized by chemical means and was shown to have antigenic activity by radioimmunoassay.
3,767 citations
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.
Abstract: A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.
3,196 citations
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.
612 citations
612 citations