Biomedical subjects

B Fristensky

Publications and source records attributed to B Fristensky.

5 recordsLinked to original sources

PubMed1989

Characterization of a single copy gene encoding ferredoxin I from pea.

We have isolated, mapped, and sequenced a genomic clone containing the ferredoxin I (Fed-1) gene from Pisum sativum. The gene is present as a single copy per haploid genome. It has no introns, and it specifies a 753-nucleotide transcript encoding a 149-amino acid protein including a 52-residue transit peptide. Upstream sequences from Fed-1 contain several elements with similarity to transcriptional regulatory elements from RbcS and Cab genes, and gel mobility shift assays show that nuclear extracts from light-grown pea leaves contain one or more DNA binding activities specific for Fed-1 5'-flanking sequences. RbcS and Cab regulatory sequences are only weak competitors for this binding, however, and the RbcS and Cab similarities mostly lie outside of the region essential for binding. These data are discussed in terms of previously observed physiological differences between the light responses of Fed-1 and other genes.

Amino Acid Sequence↗

PubMed1987

Database bias and the identification of protein coding sequences.

A simple quantitative test for the probability that an open reading frame actually codes for a protein has been described by Tramontano and Macchiato (1986). However, their test is only valid for the special case in which both coding and noncoding sequences are represented equally. We present a generalized adaptation of their method that uses estimates for the relative proportions of coding and noncoding sequences to provide a more accurate prediction.

Amino Acid Sequence↗

PubMed1986

Improving the efficiency of dot-matrix similarity searches through use of an oligomer table.

Dot-matrix sequence similarity searches can be greatly speeded up through use of a table listing all locations of short oligomers in one of the sequences to find potential similarities with a second sequence. The algorithm described finds similarities between two sequences of lengths M and N, comparing L residues at a time, with an efficiency of L X M X N/(SK) where S is the alphabet size, and k is the length of the oligomer. For nucleic acids, in which S = 4, use of a tetranucleotide table results in an efficiency of L X M X N/256. The simplicity of the approach allows for a straightforward calculation of the level of similarities expected to be found for given search parameters. Furthermore, the storage required is minimal, allowing for even large sequences to be compared on small microcomputers. Theoretical considerations regarding the use of this search are discussed.

Amino Acid Sequence↗

PubMed1983

The nucleotide sequence of a new human repetitive DNA consists of eight tandem repeats of 66 base pairs.

Three cloned human DNA fragments obtained from a fibroblast genomic DNA were sequenced and identified as containing members of the well-known 300-bp Alu family of interspersed, middle-repetitive DNA sequences. One of these cloned DNA fragments, p16, also contains members of a new repetitive DNA family, which repeats several thousand times in the human genome. Each member of the new 528-bp family consists of eight tandem repeats of a 66-bp sequence. An AluI recognition site is present at the same location in each repeat, and a 25-bp sequence occurs twice (as a tandem repeat) in each of the eight repeats. There is no sequence homology between the new 528-bp family and the 300-bp Alu family, and the new family lacks the flanking 7- to 20-bp direct repeats as well as the dAMP-rich sequences characteristic of the 300-bp Alu family. Construction of a putative evolutionary tree indicates that six duplication events are needed to give rise to the eight tandemly repeated 66-bp units in the new 528-bp family.

Base Sequence↗

PubMed1982

Portable microcomputer software for nucleotide sequence analysis.

The most common types of nucleotide sequence data analyses and handling can be done more conveniently and inexpensively on microcomputers than on large time-sharing systems. We present a package of computer programs for the analysis of DNA and RNA sequence data which overcomes many of the limitations imposed by microcomputers, while offering most of the features of programs commonly available on large computers, including sequence numbering and translation, restriction site and homology searches with dot-matrix plots, nucleotide distribution analysis, and graphic display of data. Most of the programs were written in Standard Pascal (on an Apple II computer) to facilitate portability to other micro-, mini-, and and mainframe computers.

Base Sequence↗