Introduction to the Workshop
URLs Provided by Attendees

Abstracts

Mapping

Informatics

Sequencing

Instrumentation

Ethical, Legal, and Social Issues

Infrastructure

The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.

Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.

Analysis of Randomly Cloned Chromosome 5 DNA Sequences for Similarities to GenBank Sequences

Robert Wagner, Deborah Grady, Julie Houts, Donna Robinson, Joe Gatewood, Sue Thompson, Larry Deaven, and Robert Moyzis.
Life Sciences Division and The Center for Human Genome Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545

In order to generate a framework STS map of human chromosome 5, approximately 761 random DNA segments from chromosome 5 (Chr5seqs) were cloned in M13mp18. They averaged 250bp in length, and were sequenced with a Dupont Genesis 2000 automated sequencer. A total of 39 (5.9%) Chr5seqs were found to have open reading frames (ORFs) using the GRAIL program; five of these were all L1 and one was all Alu. After eliminating from the total 761 all those sequences that were all Alu, L1, vector or not sequenceable, 445 of the remaining 72% (545) sequences, were subjected to similarity determinations against all sequences in GenBank using the INHERIT program. An INHERIT similarity score of 200 (corresponding to approximately 90% similarity) or better with various GenBank sequences was found for 42% (187) of these 445 sequences. About 100 of these were also subjected to analysis with the BLASTGA program searching for similarities of length greater than 60% that had identities greater than 70% of alignment length. The combined results of both searches may be summarized as follows: (1) Five sequences have been identified that have significant similarities to genes known to be on chromosome 5, and map to loci previously identified for them. This is as expected given that approximately one percent of the genes likely to be present on chromosome 5 have been sequenced. (2) At least ten Chr5seqs show significant similarity for specific regions of a number of different seemingly unrelated genes. (3) A number of known repeats such as pTR5 have been identified which have ORFS. (4) Several Chr5seqs showed close similarity with protein encoding sequences of genes in GenBank not previously known to have loci on Chromosome 5. As an example one sequence with an ORF has about 90% similarity for the gene HUMHSD that encodes delta-5-3-beta-hydroxy-delta-5-steroid dehydrogenase on 1p13.1. This sequence also shows similarity for cognate genes in four other mammals, indicating that an HSD family member or pseudogene resides on chromosome 5.