A comprehensive set of sequence analysis programs for the VAX
TLDR
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.read more
Citations
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Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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.
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Mfold web server for nucleic acid folding and hybridization prediction
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).
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The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
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.
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In vitro selection of RNA molecules that bind specific ligands.
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.
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The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
Brenda J. Reinhart,Frank J. Slack,Frank J. Slack,Michael Basson,Amy E. Pasquinelli,Bettinger Jc,Ann E. Rougvie,H R Horvitz,Gary Ruvkun +8 more
TL;DR: It is shown that let-7 is a heterochronic switch gene that encodes a temporally regulated 21-nucleotide RNA that is complementary to elements in the 3′ untranslated regions of the heteroch chronic genes lin-14, lin-28, Lin-41, lin -42 and daf-12, indicating that expression of these genes may be directly controlled by let- 7.
References
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A general method applicable to the search for similarities in the amino acid sequence of two proteins
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Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
Michael Zuker,Patrick Stiegler +1 more
TL;DR: In this article, a dynamic programming algorithm was proposed to fold an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies, based on applied mathematics.
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Proceedings of the National Academy of Sciences
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Codon catalog usage is a genome strategy modulated for gene expressivity
TL;DR: The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added, and internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.
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Recognition of protein coding regions in DNA sequences
TL;DR: The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time.