遗传学实验技术

Multiple sequence alignment is one of the most challenging lems in biocomputing. Sequence comparison, averaging, and so ticated editing are required to make the computer do wha researcher wants to do. However, frequently complaints are that an alignment is “bad” or “insufficient” if calcu ...

Comparison of sequences can be done in various ways. Biological sequences differ in length and composition. Whereas simple identity is relatively easy to compute, “similarity” must be defined before a computer can start its calculation. A simple identity matrix for DNA sequences is shown in ...

Sequence information in the computer needs to be stored in a formatted way in order to accommodate the following features specific to this data type: 1. Sequence name. 2. Comments (e.g., reference information).

As mentioned in Chapter 3, restriction maps are generated on a computer using programs that match your sequence against a predefined sequence (referred to as “enzymes”). Positive hits are displayed as a function of the sequence coordinate plotted vs the patterns found. In order to view the result ...

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 ...

Drawing circular restriction maps is a multistep procedure. First, primary data are collected with a pattern matching program that runs like the ones used in linear restriction map generation (see Chapter 3) Second, these data are restructured and displayed as graphics. Additional data c ...

Many noncommercial software packages and individual programs are available at several computer sites around the world. Some sites make these files available via “file-servers,” and some via “anonymous FTI?” There are usually information files available listing everything that can ...

Many noncommercial software packages and individual programs are available at several computer sites around the world. Some sites make these files available via “file-servers,” and some via “anonymous FTI?” There are usually information files available listing everything that can ...

A “sequence format” is a punctuation style, or defined layout of text, within a computer file that separates a sequence from everything else. It allows computer programs that “understand” the format to distinguish between the sequence and any reference documentation also in the file. Some for ...

As this volume illustrates, computers have become an integral tool in the analysis of DNA and protein sequence data. One of the most popular applications of computers in modern molecular biology is to characterize newly determined sequences by searching DNA and protein sequence database ...

The PC/GENE package contains several programs that scan nucleic acid sequences for predefined functional sites or sequence motifs. These include EUKPROM, which searches for a TATA-box, a Cap signal, a CCAAT-box, and a GC-box. Also included is SIGNAL which searches for splice junctions, euka ...

Generally, when a new sequence is found, it is important to know if all or parts of it are similar to other known sequences. This can be done by using the new sequence to search for similarity to sequences in a database. The PC/GENE package contains two programs, FSTNSCAN and FSTPSCAN, for searching nucleic ac ...

Generally, the purpose of aligning sequences is to determine the phylogenetic relationship between the sequences and/or to identify conserved regions that may represent biologically functional domains. The PC/GENE package contains three programs that help to determine the opt ...

Translation of a nucleic acid sequence into a polypeptide sequence is required in a variety of situations. For example, when performing a DNA sequencing project, one frequently will translate the sequence in order to search for open reading frames. If open reading frames are found, it is desirab ...

Analysis of a nucleotide sequence using restriction endonucleases is perhaps one of the most basic functions carried out by various sequence analysis software programs. The PC/GENE programs provide a comprehensive coverage of various protocols related to the restriction endonu ...

The PC/GENE package of sequence management and analysis software provides a comprehensive set of over 70 programs capable of performing all of the analyzes routinely required by the molecular biologist. The software is distributed by IntelliGenetics, Inc., 700 East El Camino Real, Mount ...

To produce a restriction map using a computer program a single sequence (your target sequence) is matched against a predefined sequence pattern database (referred to as “enzymes”). The pattern database used must obey some rules with respect to the pattern definition language, and what an ind ...

MicroGenie can compare two sequences to detect regions of homology between them and can align two or more sequences, inserting gaps if necessary to improve the alignment. The procedures to do this are in the Compare section. A sequence (DNA or protein) can be searched for homologies against a data bank ...

At an initial inspection, MicroGenie appears to have a limited range of procedures designed specifically to analyze proteins; however, many of its procedures can be used with both proteins and nucleic acids. By suitable selection of control parameters, the protein analysis procedures c ...

MicroGenie can translate DNA to protein, either as output from procedures in the Analysis section or, in the Entry section, by making a new protein sequence file translated from a nucleic acid sequence file. If a DNA sequence needs to be translated into protein to undertake further analysis or manip ...