Cryptography as Applied to a Unix Environment. OLIVER DARIO (Contra Costa College San Pablo, CA 94806) CHARLIE VERBOOM (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Cryptography is known as the act of enciphering and deciphering messages in secret code. In today's computer systems and networks, the act of enciphering and deciphering messages is applied to the bits of data that we share across networks. The threat imposed on our computer systems by attackers is the primary reason that we have to send messages, or data, in secret code. In its default state, email is typically sent through the Internet as clear text, or unencrypted, which means that a sent message can easily be made viewable. Remote connection protocols such as FTP and Telnet are susceptible to various attacks, such as the man-in-the-middle attack, due to their lack of data encryption during their sessions. The application of cryptography to today's computer systems and networks helps to ensure that electronic information remains in its original form while being delivered, and that it is not falsified in order to gain access to a remote computer. The following research paper is an analysis of the cryptographic methods supported by the Secure Shell protocol (SSH), a replacement for Telnet, and GNU Privacy Guard (GnuPG), a cryptographic method applied to email messages.

Identification of CRISPR Elements in Prokaryotes Using Suffix Trees. TERESA RAMSEY (Jackson State University Jackson, MS 39217) NIKOS KYRPIDES/PHIL HUGENHOLTZ (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Recently, a new class of repeats have been studied. CRISPRs, which are clustered regularly interspaced short palindromic repeats, are repetitive sequences interspaced by similarly sized non-repetitive spacer sequences ranging in sizes from 21 to 37 base pairs. The identification of these repeats have been analyzed manually by previous researchers. In our study, we create a tool, CRISPR Recognition Tool (CRT), that uses suffix trees to identify CRISPRs. We identified other known repeat finders and compared the running time of those tools to that of CRT. Our results show CRT to be the optimal tool when searching for CRISPR elements.

NIS and NFS security - An introduction to a secured NIS and NFS. NOPPOL SETOBOL (Contra Costa College San Pablo, CA 94806) CHARLES VERBOOM (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Laboratories today typically consist of having a couple of workstations that are assigned to specific scientists for that department. These workstations are independent of each other and do not share files unless manually transferred from one workstation to another. Account management configuration and data backup must to be done manually for every machine. An alternative to this setup is using a Linux client-server model implemented with Network Information Services (NIS) and Network File Systems (NFS). These services allow client workstations to have the same configuration files and file systems. User account information and home directories will exist on all configured workstations that are configured with these two services. Managing accounts and backing up data is easily done from the server. Unfortunately, there are a lot of security vulnerabilities that exist when using these two protocols. The following research paper will discuss the stability, vulnerability and comparison of NIS and NFS client-server model to a secured independent workstation. The results will determine whether a client-server model with NIS and NFS can be as secure as an independent workstation in a working environment.

The Identification and Characterization of CRISPR patterns in Prokaryotic DNA. FAREEDAH SABREE (Jackson State University Jackson, MS 39217) NIKOS KYRPIDES (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

CRISPRs are clustered regularly interspaced short palindromic repeats commonly found in the DNA of prokaryotic cells. CRISPRs are comprised of multiple short direct nucleotide repeats that range in size from 21 to 37 base pairs, and are interspaced by similarly sized non repetitive DNA sequences. They possess a common leader sequence that is usually adjoined along either side of the CRISPR pattern. In this paper, we discuss our extensions to the work of Jansen et al. They found more than forty prokaryotic species with CRISPR patterns. We extend their research by re-examining the organisms found by them and searching for new patterns in some species that have been sequenced since their research was completed in 2002. We use the computer software, CRISPR Recognition Tool (CRT), which we developed to find CRISPR patterns along with the Integrated Microbial Genomes (IMG) system (Joint Genome Institute's (JGI) data management system). Upon finding new CRISPR patterns, we characterize and compare them to previous results of other studies. When comparing, we take into consideration the length and the frequency of the patterns. From our search of CRISPR patterns, we found these characteristics: from the 27 organisms, the repeat length ranged in size from 19 in Yersinia pestis KIM to 37 base pairs in Thermus Thermophilis HB27, Porphyromonas gingivalis W83, and Methylococcus Capsulatus BATH. Also, the largest CRISPR loci found was Geobactersulfurreducens PCA with 143 repeats. Overall, the average repeat length of the CRISPR was 32 base pairs. Hopefully, CRT will aid in the discovery of the biological function of CRISPR patterns.