Basic Protocol Using The Neighbor Program From The Phylip Package To Construct A Phylogenetic Tree

This protocol describes the use of NEIGHBOR (see Fig. 6.3.1), included in the PHYLIP 3.6 package, which is distributed by Joe Felsenstein (University of Washington) and is one of the most widely used software packages in phylogeny studies. NEIGHBOR is the PHYLIP implementation of Neighbor Joining (Saitou and Nei, 1987). Distance estimation is performed using DNADIST or PROTDIST (Support Protocols 1 and 2). To accomplish the bootstrap procedure, first resample the sites using SEQBOOT (Support...

Blocks

Block Maker finds conserved blocks in a group si two or more unaligned protein sequences, which are assumed Co be related, using two different algorithms. At least two protein sequences must be provided to make blocks. Each sequence must have a unique name of 10 characters or Iess. If you have the accession nuiinbers of some sequences you would like to use. Batch Fntre can create a file for you In FASTA tormaf. nfcer your email address you want the results through email Enter a short...

Guidelines For Understanding Results

This section presents a description of a detailed OMIM entry, describing the location and types of data returned from a simple or complex OMIM query. For this example, OMIM *163890 (alpha synuclein) will be discussed. The OMIM Accession Number and Header Each OMIM entry is assigned a unique MIM number. The numbering system uses the first number to indicate the mode of inheritance of the disorder as described in Table 1.2.3. The distinction between 1 or 2 and 6 is that entries catalogued before...

Alternate Protocol 2 Finding Repeated Motifs In Dna Sequences With Meme

This protocol describes the use of MEME via the MEME Web interface or the command line to discover repeated motifs in a set of DNA sequences. It also discusses how to interpret the motifs and use them to search sequence databases. Command-line MEME works on many uniprocessor computers, some multiprocessor computers, and clusters that have the MPICH message-passing software installed. A list of supported operating systems and their manufacturers is available at (optional). Software Web browser...

Basic Protocol Searching Omim Over The Internet

OMIM may be accessed directly from the NCBI home page (http www.ncbi.nlm.nih.gov) by clicking on the OMIM link in the blue bar at the top of the page. This protocol describes accessing the Web site and entering search terms to retrieve OMIM records. It then briefly reviews the format of an OMIM record and guides the user through the numerous hyperlinks that are available. The search term synuclein will be used as an example throughout this protocol. Any Internet-connected computer Software...