遗传学实验技术

CLUSTAL is a package for performing fast and reliable automatic multiple alignment of many DNA or protein sequences. It was originally written for IBM-compatible microcomputers (1,2) and was later reorganized as a single program for VAX mainframes. Recently (3), the package was complete ...

Early attempts to use quantitative measures to provide information on divergent evolution of macromolecules include estimates, such as the degree of crossreactivity of antisera to purified proteins (1,2), the degree of interspecific hybridization of DNA (3), and differences in pep ...

Several approaches to the multiple alignment problem are conceivable, but virtually all are based on the Parsimony Principle: Choose the history of a set of sequences that minimizes the overall amount of change (insertion-deletions and substitutions/mutations). This formulation ...

In this chapter we give an overview of the chapters on the “Staden Package” of programs. Here the equipment required is described, and the scope of the package and the user interfaces is outlined. The next chapter covers character sets, sequence formats, and sequence library access.

The EMBL Data Library (1) was founded in 1980 as a direct consequence of the amount of sequence data appearing in the journals. Over the past 11 years, the growth in data acquisition has been exponential. With the latest developments in genome projects, we foresee no let up in the amount of data they will recei ...

Data input, assembly, checking, and editing are the major tasks of sequence project management. Data input is described in a previous chapter and everything else is covered here. The programs can deal with data derived from autoradiographs and from sequencing machines, such as the Applied Bio ...

The program NIP contains a routine for finding and displaying the positions of the cut sites of restriction enzyme recognition sequences. Linear or circular sequences can be searched, and the results can be listed in various forms or displayed graphically. The recognition sequences to be se ...

This chapter deals with performing simple statistical and structural analysis of nucleotide sequences, and also describes some more unusual tests. Base, dinucleotide and codon compositions, potential amino acid compositions, and the relative frequencies of each base in each pos ...

This chapter deals with producing simple listings from nucleotide sequences. All functions are contained in the program NIP. Sequences can be listed alone, in single- or double-stranded format, or with translations to protein. The translations can be of all six phases, all open reading frame ...

The program NIP contains several ways of defining and searching for motifs (1–4), and also contains a number of “hardwired” motifs that are already defined and can be selected as separate searches. Searches for percentage matches to consensus sequences, the use of score matrices, and the creati ...

Here is described one of the most powerful facilities provided by the program NIP: the ability to define and search for complex patterns of motifs (1–3). Chapter 8 gives details of searching for individual motifs, but this chapter shows how to create patterns and libraries of patterns, and to use them to s ...

Recent breakthroughs in multiplexed SNP (single nucleotide polymorphism) genotyping technology have enabled global mapping of the relationships between genetic variation and disease. Discoveries made by such whole-genome association studies often spur further inter ...

Transfusion recipients who become alloimmunized to blood group antigens require antigen-negative blood to limit adverse transfusion reactions. An alternative strategy to phenotyping blood is to assay genomic DNA for the associated single nucleotide polymorphisms (SNPs). A m ...

During the last decade, blood bank specialists have shown an increased interest in molecular analyses to complement serology work in determining blood group antigens. To efficiently respond to the numerous demands made for hemolytic disease of the newborn cases and polytransfused pa ...

GENEMAN is the LASERGENE module for DNA, protein, Genetic MedLine (American National Library of Medicine, Bethesda, MD) and structural (Brookhaven) database searching (see Note 1). Newly derived DNA sequences and their protein ORFs should routinely be checked against the relevant dat ...

This chapter describes the analysis and assembly of sequence data generated by the Applied Biosystems (ABI, Foster City, CA) automated sequencer after sequencing PCR products using Taq dye terminators (e.g., with the PRISM DyeDeoxy Terminator cycle sequencing kit). We use Taq dye termina ...

AutoAssembler is a Macintosh software package from PE-Applied Bio-systems (Foster City, CA) designed for assembly of DNA sequences. The graphical user interface is easy to use and allows the importation of text riles as well as analysis files from Applied Biosystems automated sequencers ...

There are multiple situations in the context of transfusion medicine where the classic serologic methods are unable to provide an adequate response, for example, recently polytransfused patients, patients with positive direct human antiglobulin tests, and hemolytic disease of t ...

The minisequencing multiplex reaction to genotype ABO blood group system is described and discussed. This method was found to be a reproducible strategy to type 6 common alleles (A1, A2, B, 01, 01 V, and 02) of the ABO blood group system, the high specificity and sensitivity make it suitable also in forensic ...

Most human platelet alloantigen (HPA) systems comprise biallelic single nucleotide polymorphisms in genes encoding major membrane glycoproteins. Genotyping for these systems is required in the investigation of patients with suspected HPA antibodies and for the provision of c ...