Biomedical subjects

J Ostell

Publications and source records attributed to J Ostell.

4 recordsLinked to original sources

PubMed1992

GeneScape: a relational database of Escherichia coli genomic map data for Macintosh computers.

We present a relational database program developed in FoxBase+/Mac for the viewing and manipulation of ordered restriction maps and associated features of the Escherichia coli genome including sequenced genes and the Kohara miniset of bacteriophage lambda clones. Use of this program allows easy access to the wealth of information being collected in a dataset of DNA sequences, maps and genetic data known as EcoSeq, EcoMap and EcoGene respectively.

Algorithms↗

PubMed1991

Mapping sequenced E.coli genes by computer: software, strategies and examples.

Methods are presented for organizing and integrating DNA sequence data, restriction maps, and genetic maps for the same organism but from a variety of sources (databases, publications, personal communications). Proper software tools are essential for successful organization of such diverse data into an ordered, cohesive body of information, and a suite of novel software to support this endeavor is described. Though these tools automate much of the task, a variety of strategies is needed to cope with recalcitrant cases. We describe such strategies and illustrate their application with numerous examples. These strategies have allowed us to order, analyze, and display over one megabase of E. coli DNA sequence information. The integration task often exposes inconsistencies in the available data, perhaps caused by strain polymorphisms or human oversight, necessitating the application of sound biological judgment. The examples illustrate both the level of expertise required of the database curator and the knowledge gained as apparent inconsistencies are resolved. The software and mapping methods are applicable to the study of any genome for which a high resolution restriction map is available. They were developed to support a weakly coordinated sequencing effort involving many laboratories, but would also be useful for highly orchestrated sequencing projects.

Base Sequence↗

PubMed1990

Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.

We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.

Amino Acid Sequence↗

PubMed1990

An algorithm for searching restriction maps.

This paper presents an algorithm that searches a DNA restriction enzyme map for regions that approximately match a shorter 'probe' map. Both the map and the probe consist of a sequence of address-enzyme pairs denoting restriction sites, and the algorithm penalizes a potential match for undetected or missing sites and for discrepancies in the distance between adjacent sites. The algorithm was designed specifically for comparing relatively short DNA sequences with a long restriction map, a problem that will become increasing common as large physical maps are generated. The algorithm has been used to extract information from a restriction map of the entire Escherichia coli genome.

Algorithms↗