Mapping sequencedE.coligenes by computer: software, strategies and examples

Abstract

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.

Modulation of acid-induced amino acid decarboxylase gene expression by hns in Escherichia coli

“…1 were observed. We derived a 9-kb restriction fragment from these maps and conducted a computer map search with the programs kindly provided by Kenneth E. Rudd (20,21). The highest-score alignment was found to be contains most of the hns gene sequence (see Fig.…”

Roles of SpoT and FNR in NH4+ assimilation and osmoregulation in GOGAT (glutamate synthase)-deficient mutants of Escherichia coli

“…L10328) in the EMBL DNA sequence database, at 82.2 centisomes on the E. coli physical map (data not shown; see Fig. 3) (4,29,40,44). This region includes two unidentified open reading frames (ORF_o223 and ORF_f562) and the complete sequence of the first three genes (spoR or gmk, rpoZ, and spoT) of the spoT operon (Fig.…”

An efficient algorithm for identifying matches with errors in multiple long molecular sequences

“…† Location of the word in the genome scaled 0 to 100 clockwise from the origin of replication (Bachmann, 1990). ‡ Rudd et al (1990Rudd et al ( , 1991. I designates that the interval containing the long word is in the same polarity as the coding polarity of the neighboring genes; D designates that the interval and the neighboring genes have been inverted and complemented (dyad); ?…”

“…The performance of the program was tested with a database of E. coli DNA sequences totalling 1,431,059 bp (Rudd et al, 1991). The database contains 389 sequences altogether.…”

“…We have applied our general program to the E. coli DNA contig collection developed by Rudd et al (1990Rudd et al ( , 1991. This database consists of all the E. coli sequences) in GenBank (plus a few unpublished sequences) from which all duplicates have been removed and all established overlapping sequences have been appropriately joined.…”