Computer programs for the analysis and the management of DNA sequences.

A program package is described for the management and the analysis of DNA sequence data. The programs - with the exception of a few Fortran routines - are written in the programming language APL. They are best used interactively although batch processing is possible. The package has been in constant use for about 3 years and contains programs for most of the routine problems presently found in a DNA sequencing laboratory.     

A convenient and adaptable microcomputer environment for DNA and protein sequence manipulation and analysis.

We describe the further development of a widely used package of DNA and protein sequence analysis programs for microcomputers (1,2,3). The package now provides a screen oriented user interface, and an enhanced working environment with powerful formatting, disk access, and memory management tools. The new GenBank floppy disk database is supported transparently to the user and a similar version of the NBRF protein database is provided. The programs can use sequence file annotation to automatically annotate printouts and translate or extract specified regions from sequences by name. The sequence comparison programs can now perform a 5000 X 5000 bp analysis in 12 minutes on an IBM PC. A program to locate potential protein coding regions in nucleic acids, a digitizer interface, and other additions are also described.     

An integrated family of amino acid sequence analysis programs

During the last years abundant sequence data has become availabledue to the rapid progress in protein and DNA sequencing techniques.The exact three-dimensional structures, however, are availableonly for a fraction of proteins with known sequences. For manypurposes the primary amino acid sequence of a protein can bedirectly used to predict important structural parameters. However,mathematical presentation of the calculated values often makesinterpretation difficult, especially if many proteins must beanalysed and compared. Here we introduce a broad-based, user-definedanalysis of amino acid sequence information. The program packageis based on published algorithms and is designed to access standardprotein data bases, calculate hydropathy, surface probabilityand flexibility values and perform secondary structure predictions.The data output is in an ‘easy-to-read’ graphicformat and several parameters can be superimposed within a singleplot in order to simplify data interpretations. Additionally,this package includes a novel algorithm for the prediction ofpotential antigenic sites. Thus the software package presentedhere offers a powerful means of analysing an amino acid sequencefor the purpose of structure/function studies as well as antigenicsite analyses. These algorithms were written to function incontext with the UWGCG (University of Wisconsin Genetics ComputerGroup) program collection, and are now distributed within thatpackage. Received on March 20, 1987; accepted on September 4, 1987     

The current status and portability of our sequence handling software.

I describe the current status of our sequence analysis software. The package contains a comprehensive suite of programs for managing large shotgun sequencing projects, a program containing 61 functions for analysing single sequences and a program for comparing pairs of sequences for similarity. The programs that have been described before have been improved by the addition of new functions and by being made very much easier to use. The major interactive programs have 125 pages of online help available from within them. Several new programs are described including screen editing of aligned gel readings for shotgun sequencing projects; a method to highlight errors in aligned gel readings, new methods for searching for putative signals in sequences. We use the programs on a VAX computer but the whole package has been rewritten to make it easy to transport it to other machines. I believe the programs will now run on any machine with a FORTRAN77 compiler and sufficient memory. We are currently putting the programs onto an IBM PC XT/AT and another micro running under UNIX.     

SeeDNA： A Visualization Tool for K-string Content of Long DNA Sequences and Their Randomized Counterparts

An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK support. It displays two-dimensionai (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK package is freely available.     

Objective classification and analysis of vegetation data

A program package is described in which vegetation data can be objectively classified and analysed. Classification is based on minimum entropy. Results show that in a comparison with TWINSPAN, improvements to the relevé sequence, in terms of community variation, can be obtained. Furthermore, TWINSPAN classifications are shown to be dependent on a particular relevé input sequence.     

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. Availability and implementation: JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.     

ANTHEPROT 2.0: A three-dimensional module fully coupled with protein sequence analysis methods

ANTHEPROT is a fully interactive graphics program devoted to the analysis of the sequences and structures of proteins. This program, originally developed to facilitate the protein sequence analysis coupled with multiple alignments and predicted secondary structures of proteins,^1,2 now comprises a powerful 3D module to display and handle macromolecular structures. All the methods that were previously integrated into ANTHEPROT are now directly coupled with a 3D window that provides the user all the classic features of a molecular modeling package. Indeed, it allows real-time rotation and translation of 3D structures with many kinds of models in depth-cueing mode (space filling, backbone, wire models, main chain, and ribbons), selections (atom type, residue type, segments, and chain), colorcoding systems (amino acid properties, predicted or observed secondary structures, temperature B factor, and subunits), geometric calculations (Ramachandran plot, distances, and angles), and fitting molecules. Stereo views are possible as well as HPGL standard files. A module specifically devoted to the determination of 3D structures using nuclear magnetic resonance is also available. This major release of our program for IBM rs6000 workstations is available by anonymous ftp to ibcp.fr for academic institutions.     

PHYTOTAB — A program package for Braun-Blanquet tables

A computer program package of six programs for vegetation classification is described. The package includes raw field-data input, automatic and user sequencing modes, final table and synoptic table preparation which are camera-ready and also allows the user the option of ordinating by means of DECORANA.     

Cloning and structural characteristics of human hair keratin genes rich in sulfur]

Two human genomic genes for the hair high-sulphur keratins were for the first time cloned in a 15 kb fragment. The primary structures of the coding regions of the genes and their 5'- and 3'-flanks were determined. In the 5'-flanking region, TATA boxes, initiating codons and a 18 nucleotide sequence, previously described in sheep keratin genes and designated as "the matrix-specific" sequence was revealed. Basing on the nucleotide sequences, the encoded amino acid sequences of the high-sulphur keratins were determined for the first time. The suggested functional role of the structural elements (regions) revealed in the proteins primary structure and problems concerning their evolution tendencies are discussed.     

The locally optimal method of cyclic alignment to reveal latent periodicities in genetic texts. The NAD-binding protein sites

A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying the apparent regularity in their secondary structures, not being obvious at the primary structure level.     

The Locally Optimal Method of Cyclic Alignment to Reveal Latent Periodicities in Genetic Texts: the NAD-binding Protein Sites

A program package has been developed to search for hidden tandem repeats of any specified type in the protein sequence databases. The applied algorithm of the locally optimal cyclic alignment is able to find subsequences possessing a certain profile-based periodicity type when no appreciable homology between periods is observed, as well as in the presence of arbitrary insertions/deletions. The profile can be adjusted to search for the periodicity types structurally and functionally important. The Swiss-Prot database has been analyzed to reveal the periodicities undetectable earlier that are caused by the secondary and super-secondary structure regularities of the NAD-binding sites. In particular, a significant periodicity of 24 aa was found to be characteristic of the absolute majority of domains possessing the Rossman (or Rossman-like) fold and displaying apparent regularity in their secondary structures, not being obvious at the primary structure level.     

SOMAP: a novel interactive approach to multiple protein sequences alignment

A novel interactive method for generating multiple protein sequencealignments is described. The program has no internal limit tothe number or length of sequences it can handle and is designedfor use with DEC VAX processors running the VMS operating system.The approach used is essentially one of manual sequence manipulation,aided by built-in symbolic displays of identities and similarities,and strict and ‘fuzzy’ (ambiguous) pattern-matchingfacilities. Additional flexibility is provided by means of aninterface to a publicly available automatic alignment systemand to a comprehensive sequence analysis package. Received on August 28, 1990; accepted on November 20, 1990     

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

Background  

Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment.     

Bio3d: an R package for the comparative analysis of protein structures

An automated procedure for the analysis of homologous protein structures has been developed. The method facilitates the characterization of internal conformational differences and inter-conformer relationships and provides a framework for the analysis of protein structural evolution. The method is implemented in bio3d, an R package for the exploratory analysis of structure and sequence data. AVAILABILITY: The bio3d package is distributed with full source code as a platform-independent R package under a GPL2 license from: http://mccammon.ucsd.edu/~bgrant/bio3d/     

A program package applicable to the detection of overlaps between restriction maps.

A computer program package for the storage, change, and comparison of restriction maps is described. The programs are intended to detect overlaps between relatively short (about 10-40 kb; abbreviations ref.2) maps and to merge the overlapping fragments into large restriction maps. They run on a 16-bit-microcomputer with limited memory and addressing capability. Due to the restricted reliability of restriction maps compared with DNA sequence data a particular storage method was used. The source code of the programs is freely available (+).     

STATSEARCH: a GCG-compatible program for assessing statistical significance during DNA and protein databank searches

We describe a program STATSEARCH which implements the methodof Mott et al. (1989) for searching DNA and protein sequencedatabanks for statistically significant similarities to a givenquery sequence. STATSEARCH is written to run in conjunctionwith the GCG sequence analysis package.