Author
John Devereux
Bio: John Devereux is an academic researcher from University of Wisconsin-Madison. The author has contributed to research in topics: Gene & Amino acid. The author has an hindex of 7, co-authored 7 publications receiving 16896 citations.
Topics: Gene, Amino acid, Genetic code, Globin, Genomic library
Papers
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TL;DR: A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system.
Abstract: The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.
14,575 citations
Book•
01 Jan 1991
TL;DR: The Sequence Analysis Primer as mentioned in this paper provides the necessary background to enter this exploding field and helps more seasoned researchers to fine-tune their approach, covering basic data manipulation, and offers valuable advice for overcoming common problems.
Abstract: Computerized sequence analysis is an integral part of biotechnological research, yet many biologists have received no formal training in this important technology. Sequence Analysis Primer offers the necessary background to enter this exploding field and helps more seasoned researchers to fine-tune their approach. Compatible with most sequence analysis programs, the primer covers basic data manipulation, and offers valuable advice for overcoming common problems. A detailed example giving steps for characterizing a new gene sequence provides users with "hands-on" experience when combined with their current software.
1,496 citations
TL;DR: The codon preference plot is useful for locating genes in sequenced DNA, predicting the relative level of their expression and for detecting DNA sequencing errors resulting in the insertion or deletion of bases within a coding sequence.
Abstract: The codon preference plot is useful for locating genes in sequenced DNA, predicting the relative level of their expression and for detecting DNA sequencing errors resulting in the insertion or deletion of bases within a coding sequence. The three possible reading frames are displayed in parallel along with the open reading frames and plots of the location of rare codons in each reading frame.
375 citations
TL;DR: A gene encoding one of the 19,000 dalton zein proteins from a maize genomic library constructed in Charon 4A is isolated, and a basis for microheterogeneity within the gene family is identified.
222 citations
TL;DR: It is concluded that ilvIH and ilvG-region K evolved from a common ancestor and can potentially code for an 86 amino acid polypeptide.
Abstract: ilvIH of Escherichia coli K12 codes for a valine-sensitive acetohydroxy acid synthase (AHASIII). The DNA sequence of ilvIH was determined. Open reading frames and appropriate translation signals exist for two polypeptides, one containing 565 amino acids (ilvI polypeptide) and the other 160 amino acids (ilvH polypeptide). A graphic matrix analysis shows three clearcut regions of homology between ilvI and ilvG (codes for AHASII). Within these three regions of homology, 50-60% of the amino acid sequences of AHASII and AHASIII are conserved. Inspection of the region between ilvG and ilvE (the K region) revealed that it can potentially code for an 86 amino acid polypeptide. A computer analysis shows small but significant homology between the predicted amino acid sequences of the N-terminal half of the ilvH polypeptide and the putative region K polypeptide. We conclude that ilvIH and ilvG-region K evolved from a common ancestor.
98 citations
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TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
63,427 citations
TL;DR: A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system.
Abstract: The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.
14,575 citations
TL;DR: The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large by making use of universally available web GUIs (Graphical User Interfaces).
Abstract: The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as ‘MFOLDROOT’.
12,535 citations
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: Subpopulations of RNA molecules that bind specifically to a variety of organic dyes have been isolated from a population of random sequence RNA molecules.
Abstract: Subpopulations of RNA molecules that bind specifically to a variety of organic dyes have been isolated from a population of random sequence RNA molecules. Roughly one in 10(10) random sequence RNA molecules folds in such a way as to create a specific binding site for small ligands.
8,781 citations