Specialized Sequence And Protein Databases

Many specialized sequence and protein databases are available, too some are quite small whereas others are wider in scope and larger in size. The ENZYME nomenclature database, for example, is an annotated extension of the Enzyme Commission's publication. There are also databases of enzyme properties BRENDA is a collection of enzyme functional data that intends to give a representative overview on the characteristics and variability of each enzyme, LIGAND is a database of chemical compounds and...

Cdd Bioinformatic Tool

Conserved Domain Database (Marchler-Baueret al., 2002) is a database of domains consolidating SMART, Pfam and some NCBI contributions (e.g. from COGs). CDD is available at CDD uses a set of specially constructed score matrices prepared for each conserved domain (using a multiple alignment). The score matrices are derived from the domain definitions given by the source databases (e.g. SMART). CDD search and relies on a variant BLAST called reverse-position-specific BLAST (RPS-BLAST). The field...

Discriminative Learning

In discriminative learning, the decision rule is inferred directly from the data. The objective is to optimize the parameters of the rule such that some criterion is reached. The most common optimization criterion is to minimize the number of errors made by the decision rule on the instances in T (known as empirical risk minimization). As described in Section 2, discriminative methods represent a sequence in a vector of features. Some of these methods only work with numerically valued features...

Blocks

BLOCKS (http www.blocks.fhcrc.org, Henikiff et al., 2000) is a database of highly conserved protein regions. A 'block' is defined as a contiguous segment corresponding to the most conserved regions of proteins. Such blocks are automatically detected. In contrast to PROSITE, blocks are not associated with function or with known literature, as the process is completely automated. Blocks are derived by performing multiple alignments of protein families as defined in InterPro, and searching for...

Novelty

Of further importance for the assessment of patentability is novelty. The invention must be novel otherwise no patent can be granted. Novelty is at first glance an easy concept but when looked into in more detail actually pretty complicated. The general principle is that one cannot patent what is already in the art. Inventions can be made part of the art in any way conceivable by man. Be it written, or electronically for instance though the Internet, by a product or by means of oral disclosure....

Frequency Analysis

The first property to be discussed is the relative frequency of the different symbols in a message. Typical written english has a characteristic distribution of letter frequencies. The most frequent letter is 'e' with a probability of 12.7 , then't' at 9.1 closely followed by 'a' and 'o' at 8.2 and 7.5 . At the tail of the league are 'q' and 'z' at 0.1 . (It may be noted that the scores for each letter in the game 'Scrabble' wherein players form interlocking words by laying letters on a grid...

Ofer Markman

Procognia (Israel) Ltd., 3 Habosem St., Ashdod, Israel 77610 This chapter entitled Challenges in Glycoinformatics will review new themes in describing and archiving glycostructures, their interface with the analysis tools and how to extract relevant glycomic data out of those. Glycoinformatics is the common technology and electronic language that connects the field of glycobiology. It allows the presentation, and the description of glycomolecules in a useful way that enables...

Patentability Of Information

While in the preceding, much emphasis has been put on the exclusion of patentability of computer programs as such, the fourth item of the exclusion list in Art. 52.2 is also of importance in the field of Bioinformatics. More precisely the prohibition on patenting information is formulated as an absence of patentability for representations of information, defined solely by the content of information. In the context of Bioinformatics this is quite an important issue, since one of the main objects...

What Are Their Relations To Glycomics And Other Omics

Glycomolecules in this chapter is a general term describing sugars, oligosaccharides, polysaccharides and glyco-conjugates (glycoproteins, glycolipids and glycoseaminogly-cans) the molecules that bind them (lectins) and the molecule that process them e.g. glycosyltransferases and glycosidases. Glycoinformatics is the general technology that store, process and analyze the information on glycomolecules. Glycomics is the interface of wet-bench glycoanalytical technology and glycoinformatics to...

Patentability Of Computers And Program Therefore

One of the latest leading case law is the Decision of Technical Board of Appeal 3.5.1 dated 1 July 1998 (T1173 97). Herein, it is stated that a computer program product is not excluded from patentability ( . . . ) if, when it is run on a computer, it produces a further technical effect which goes beyond the normal physical interactions between program (software) and computer (hardware). In this respect, the normal interaction of a computer refers to the physics that is needed to operate a...

Yakir Benny

DEPARTMENT OF STATISTICS, THE HEBREW UNIVERSITY OF JERUSALEM, ISRAEL E-mail msby mscc.huji.ac.il ZUCCHI CLAUDIA DEPARTMENT OF CHEMISTRY, UNIVERSITY OF MODENA AND REGGIO EMILIA, VIA CAMPI, 183, I-41100 MODENA, ITALY E-mail Zucchi unimore.it Active site the truedimensional location in an enzyme or in a functional protein where the actual activity takes place (usually where the enzymatic reaction happens see site) Algorithm An algorithm is a procedure for solving a problem. The word derives from...