IBM microcomputer programs that analyze DNA sequences for tRNA genes

A set of four computer programs that search DNA sequence datafiles for transfer RNA genes have been written in IBM (Microsoft)BASIC for the IBM personal computer. These programs locate andplot predicted secondary structures of tRNA genes in the cloverleafconformation. The set of programs are applicable to eukaryotictRNA genes, including those containing intervening sequences,and to prokaryotic and mitochondrial tRNA genes. In addition,two of the programs search up to 150 residues downstream oftRNA gene sequences for possible eukaryotic RNA polymerase IIItermination sites comprised of at least four consecutive T residues.Molecular biologists studying a variety of gene sequences andflanking regions can use these programs to search for the additionalpresence of tRNA genes. Furthermore, investigators studyingtRNA gene structure-to-function relationships would not needto do extensive restriction mapping to locate tRNA gene sequenceswithin their cloned DNA fragments. Received on October 29, 1985; accepted on January 28, 1986     

Automated preparation of DNA sequences for publication.

A computer program which draws DNA sequences is described. A simple method is used which enables the user to highlight or annotate specific parts of a sequence. The sizes of the characters in the sequence to be drawn are specified by the user. In addition, vertical spacing between lines and horizontal spacing between characters can be specified. Sequences can be prepared and high quality output produced on a plotter in a short period of time, making the program advantageous to use over typing, computer printing, or preparation by a graphics department.     

Two computer programs for rapid entry of DNA sequence data

Two computer programs for the IBM personal computer are describedfor rapid and accurate entry of DNA sequence data. The DNA sequencefiles produced can be used directly by the DNA sequence manipulationprograms by R. Staden (the DataBase system), the Universityof Wisconsin Genetics Computer Group, DNASTAR, or D. Mount.The first program, DIGISEQ, utilizes a sonic digitizer for semi-automationof sequence entry. To enter the DNA sequence each band of agel reading is touched by the stylus of the sonic digitizer.DIGISEQ corrects for both changes in lane width and lane curvature.The algorithm is extremely efficient and rarely requires re-entenngthe centers of the lanes. The second program, TYPESEQ, usesonly the keyboard for input. The keyboard is reconfigured toplace nucleotides and ambiguity codes under the fingers of onehand, corresponding to the order of the nucleotides on the geldefined by the user Both programs produce individual tones foreach nucleotide, and certain ambiguity codes. This verifiesinput of the correct nucleotide or ambiguity code, and thuseliminates the need to visually check the screen display duringsequence entry. Received on November 16, 1986; accepted on June 16, 1987     

Spreadsheet-based program for alignment of overlapping DNA sequences.

Molecular biology laboratories frequently face the challenge of aligning small overlapping DNA sequences derived from a long DNA segment. Here, we present a short program that can be used to adapt Excel spreadsheets as a tool for aligning DNA sequences, regardless of their orientation. The program runs on any Windows or Macintosh operating system computer with Excel 97 or Excel 98. The program is available for use as an Excel file, which can be downloaded from the BioTechniques Web site. Upon execution, the program opens a specially designed customized workbook and is capable of identifying overlapping regions between two sequence fragments and displaying the sequence alignment. It also performs a number of specialized functions such as recognition of restriction enzyme cutting sites and CpG island mapping without costly specialized software.     

PERFILS: a program for the quantitative treatment of footprinting data

PERFILS, a computer program written in Borland TurboPascal,performs quantitative analysis of footprinting experiments usingany IBM PC or compatible microcomputer. The program uses theheight of the bands obtained from densitometric scanning offootprinting autoradiographs to calculate a differential cleavageplot. Such a plot displays, on a logarithmic scale, the differenceof susceptibility of a DNA fragment to DNase I, or any othercleaving agent, in the presence of any ligand versus the sequence.PERFILS calculates the fractional cleavage values for controland ligand, giving a table of values for each internucleotidicbond and rendering the differential cleavage plot in only afew seconds.     

Fast computer search for similar DNA sequences.

An extremely fast method of searching a nucleic acid sequence database against a probe sequence is described. The method is based on the detection of deviation from expected number and deviation from random spatial distribution of sub-sequences which are unique within a sequence, and shared between that sequence and the probe. On an IBM 3081 computer, total search of an encoded form of the EMBL nucleic acid sequence database with a 1 kbase probe sequence is completed in a few seconds. Previous best methods for a similar task required a few minutes.     

A tool for aligning very similar DNA sequences

Results: We have produced a computer program, named sim3, thatsolves the following computational problem. Two DNA sequencesare given, where the shorter sequence is very similar to somecontiguous region of the longer sequence. Sim3 determines sucha similar region of the longer sequence, and then computes anoptimal set of single-nucleotide changes (i.e. insertions, deletionsor substitutions) that will convert the shorter sequence tothat region. Thus, the alignment scoring scheme is designedto model sequencing errors, rather than evolutionary processes.The program can align a 100 kb sequence to a 1 megabase sequencein a few seconds on a workstation, provided that there are veryfew differences between the shorter sequence and some regionin the longer sequence. The program has been used to assemblesequence data for the Genomes Division at the National Centerfor Biotechnology Information. Availability: A version of sim3 for UNIX machines can be obtainedby anonymous ftp from ncbi. nlm. nih. gov, in the pub/sim3 directory. Contact: For portable versions for Macs and PCs, contact zjing@sunset.nlm. nih. gov.     

A computer program that simulates cloning of DNA

Easy Cloner is a computer program that manipulates DNA sequences as in cloning experiments and produces maps of the resulting plasmids. The program runs in the graphics mode of an IBM PC or compatible computer and is operated by using a mouse to point to the required actions. The program is available in the public domain.     

A Macintosh computer program for designing DNA sequences that code for specific peptides and proteins

A computer program (PINCERS) is described for use in the design of synthetic genes and mixed-probe DNA sequences. A protein sequence is reverse translated with generation of synonymous codons at each position producing a degenerate sequence. In order to locate potential restriction enzyme sites, the degenerate sequence is searched with a library of restriction enzymes for sites that utilize any combination of synonymous codons. These sites are indicated in a map so that they may be incorporated into the synthetic gene sequence. The program allows the user to select the appropriate codon usage table for the organism of interest and then to set a threshold usage frequency below which codons are not generated. PINCERS may also be used to assist in planning the synthesis of mixed-probe DNA sequences for cross-hybridization experiments. It can identify regions of specified length with the protein sequence that have the least overall degeneracy, thereby minimizing the number of probes to be synthesized and, therefore, maximizing the concentration of a given probe sequence.     

HYLAS: program for generating H curves (abstract three-dimensional representations of long DNA sequences)

The computer program HYLAS generates from a standard DNA lettersequence a three-dimensional space curve (H curve) which embodiesthe entire information content of the original nucleotide sequence.The program can display H curves either as two-dimensional (frontand side view) projections or as stereo-pair images. The curvescan be marked at specific nucleotide locations, annotated, rotatedfor observation from any viewing angle, and manipulated forconvenient side-by-side comparisons. Unlike the cumbersome lettersequences, H curves can be drastically condensed in size withoutlosing their ability to reflect the global nucleotide-distributionpattern of the entire DNA sequence. Often, biologically importantloci can be visually identified on the H curves. HYLAS is writtenin FORTRAN with separate mainframe (IBM- VM/CMS) and microcomputer(MS-DOS) versions. It uses the Tektronix-TCS library of graphicsubroutines. Received on October 24, 1988; accepted on July 15, 1989