Comparative analysis of DNA sequence from multiple species can provide insights into the function and evolutionary processes that shape genomes. The University of California Santa Cruz (UCSC) Genome Bioinformatics group has developed several tools and methodologies in its study ...

This chapter discusses VISTA Browser and associated computational tools for analysis and visual exploration of genomic alignments. The availability of massive amounts of genomic data produced by sequencing centers stimulated active development of computational tools for a ...

The availability of an increasing number of whole genome sequences presents us with the need for tools to quickly put them into a nucleotide-level multiple alignment. Mercator and MAVID are two programs that can be combined to accomplish this task. Given multiple whole genomes as input, Mercat ...

The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a “glocal” alignment method that handles genomic rearrangements in a global alignment ...

DIALIGN is a software program for multiple alignment of DNA or protein sequences that combines global and local alignment features. During the last years, the program has been used extensively to compare syntenic regions in genomic sequences. An anchoring option speeds up the alignment pr ...

In the current genomics era, protein and DNA sequence databases are continuously growing at an exponential rate. It has become increasingly important and useful to repeat similarity searches at frequent intervals, which then retrieve larger and larger sets of results. In addition, sequ ...

PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool) derives a position-specific scoring matrix (PSSM) or profile from the multiple sequence alignment of sequences detected above a given score threshold using protein–protein BLAST. This PSSM is used to fur ...

During the past few years, retroviral vectors have become a very important and widely used means of gene transfer. In the laboratory, their use has expanded the capabilities of investigators to perform important experiments that have solved previously unanswerable biological quest ...

SV40 is a small simian virus that has been extensively used as a viral vector in mammalian cells (1–4). The viral genome is a double-stranded supercoiled DNA molecule of 5243 bp (Fig. 1A) that is packaged into a capsid containing the viral structural proteins VP1,VP2, and VP3. SV40 induces a lytic infecti ...

Vaccinia virus has been used to express many diverse genes, such as prokaryotic enzymes, eukaryotic growth factors, protozoan structural proteins, and 50 different virus gene products (for reviews, seerefs. 1–3). The widespread use of vaccinia virus as a vector owes much to the ease of generat ...

Adenoviruses have been isolated from a large number of different species (mammalian and fowl) and over 100 different serotypes have been reported, some 43 of them human. The human adenoviruses, particularly types 2, 5, and 12, have been the most extensively characterized, and these viruses have ...

McBride and Ozer (1) were the first to show that purified metaphase chromosomes could act as vectors in transferring genetic information into mammalian cells. This technique, termed chromosome-mediated gene transfer (CMGT), involves the transfer of subchromosomal fragments from ...

Type 1 herpes simplex virus (HSV-1)-based vectors, which are naturally capable of carrying large DNA fragments like the 14 kb dystrophin cDNA, have been studied for their ability to transduce muscle cells (1–5). These vectors can persist in the host cell in a nonintegrated state and can be prepared at a ...

Gene transfer to the nervous system is an attractive option to treat a wide variety of neurological insults (1–3). The expression of trophic factor and/or antiapoptotic genes may be beneficial in halting the slow neurodegeneration in such conditions as Parkinson’s disease (4,5), the rapid ne ...

Glial tumors occur as intraaxial masses in the brain and are uniformly fatal due to lack of effective therapy. Resection combined with radiation and chemotherapy fails to eradicate malignant cells infiltrating into normal brain, and recurrence at the original site is ultimately fatal. G ...

In contrast to traditional drugs that generally act by altering existing gene product function, gene therapy aims to target the root cause of the disease by altering the genetic makeup of the cell to treat the disease. Researchers have adapted several classes of viruses as gene-transfer vecto ...

A relatively recent advance in the use of recombinant baculoviruses is their use for delivery of genes and genetic elements into mammalian cells. Baculovirus vectors retrofitted with mammalian gene promoters have been shown to efficiently deliver and express genes in a broad assortme ...

For more than two decades, retroviral biology has been the most intensely studied field in virology. The retroviral genome is encoded by a 7–11 kb positivesense single-stranded RNA molecule, two of which homodimerize and package in lipid-enveloped viral particles. Following attachme ...

Vectors derived from oncoretroviruses, represented by the prototype Molo-ney murine leukemia virus (MMLV), are powerful tools for gene transfer into mammalian cells. Vectors derived from such viruses are able to carry an insert of up to 6.5 kb. Because Retroviridae and derived vectors ins ...

Hematopoietic stem cells (HSCs) are clonogenic cells capable of both self-renewal and multilineage differentiation. An efficient method for gene transfer into HSCs is required for exploring HSC biology as well as for gene therapy of hematopoietic disorders. Retroviral vectors have ...