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L Pachter

Publications and source records attributed to L Pachter.

8 recordsLinked to original sources
PubMed2001

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies.

We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.

Animals↗
PubMed2000

Domestic violence and the trauma surgeon.

BACKGROUND: Domestic violence has become increasingly recognized as a public health problem, and was declared a national epidemic by C. Everett Koop in 1992. In the United States, 1 to million women yearly suffer injuries due to domestic violence, and 30% to 50% of female homicides are committed by a present or former partner. The majority of these murder victims had either been seen in emergency rooms for prior domestic violence-related injuries, or had reported these injuries to the police. It is estimated that 50% of all acute injuries and 21% of all injuries in women requiring urgent surgery ar the result of partner abuse. DATA SOURCE: Medline and current literature review. CONCLUSIONS: Health care professionals in the emergency room are an important contact with the victims of domestic violence, and timely identification and intervention can save lives. Overall, upwards of 35% of all emergency room visits by women are the result of domestic violence, whether due to acute injury, problems during pregnancy, or stress-related complaints. Unfortunately, domestic abuse is infrequently disclosed voluntarily by the patient, and often overlooked by the treating physician. Thus, the purpose of this review is to familiarize surgeons with the presentation and management of victims of this hidden epidemic.

Child↗
PubMed2000

Human and mouse gene structure: comparative analysis and application to exon prediction.

We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of similarity in the number, size and sequence of exons and introns. We then developed an approach for recognizing genes within such orthologous regions by first aligning the regions using an iterative global alignment system and then identifying genes based on conservation of exonic features at aligned positions in both species. The alignment and gene recognition are performed by new programs called and, respectively. performed well at exact identification of coding exons in 117 orthologous pairs tested.

Amino Acids↗
PubMed2000

Active conservation of noncoding sequences revealed by three-way species comparisons.

Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human-mouse DNA comparison studies have discovered numerous conserved noncoding sequences of which only a fraction has been functionally investigated A question therefore remains as to whether most of these noncoding sequences are conserved because of functional constraints or are the result of a lack of divergence time.

Animals↗
PubMedDate not supplied

A dictionary-based approach for gene annotation.

This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.

Alternative Splicing↗