Support Protocol 4 Displaying Bootstrap Values In Paup Trees

Bootstrap values are a measure of support for a node in a tree. These are usually given as the percentage of bootstrap trees in which that node appeared. Bootstrap trees are obtained by generating a large number (typically 1000 or more) of new data sets, each obtained by randomly resampling with replacement from the original alignment, and generating a tree from each data set. In order to correctly display bootstrap values in a bootstrap tree computed using PAUP*, the user needs to tell PAUP*...

Necessary Resources

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 Web browser (e.g., Internet Explorer, Netscape Navigator) E-mail reader (e.g., Netscape Messenger) Command-line MEME (optional) MEME can be used remotely over the Web (Web MEME), with results being returned by E-mail, or it can be installed and run on the user's...

Blocks

At the Red Hutchinson Cane Er flesear& fr Center Blocks WWW server. Search your protein or DNA sequence against a Bracks Btfflfaaafi- Hfilftl (.Example of oirtjmfl Enter your mail address if you want the remits through email * Sclcct dal abase to s& artli _Blocks*_aj We recommend searching both Stocks* and Prints, Block5+ has automatic ally-generated btacks, while Prints has nand-Cfalted blocks. Optionally select cijlsrff e eclfijjjialjjs. i -i Oationalltf Mlect amount of output Summary...

Alternate Protocol 2 Search For Short Nearly Exact Matches

By using a large expected frequency (E-value) threshold (up to 1000) and other argument values optimized for matching short sequences, much faster retrieval is achieved. From the top blast page (http www.ncbi.nlm.nih.Qov BLAST), click on the link for Search for short nearly exact matches. From Current Protocols in Bioinformatics Online Copyright 2002 John Wiley & Sons, Inc. All rights reserved. CHAPTER 3 FINDING SIMILARITIES AND INFERRING HOMOLOGIES UNIT 3.3 Finding Homologs to Nucleotide...

Basic Protocol 1 Querying Entrez

The Entrez Web interface is located at http www.ncbi.nlm.nih.gov Entrez (Fig. 1.3.1). Most of the Web pages at the NCBI Web site provide a direct link to Entrez, either in a blue bar running across the top of the page or in the left-hand sidebar. The best way to illustrate the integrated nature of the Entrez system and to drive home the power of neighboring is by considering three biological examples, described in Basic Protocols 1 and 2 and the Alternate Protocol. Note that the example...

Evidence Codes and Citations

Every association made between a GO term and a gene product must be attributed to a source, and must indicate the evidence supporting the annotation. A simple controlled vocabulary is used to record evidence types it is described in the GO Evidence Codes document For a single gene product, there may be strong evidence supporting annotation to a general term, and less reliable evidence supporting annotation to a more specific term. Many of the evidence codes represent certain types of...

Alternate Protocol 1 Downloading Omim

As alluded to earlier, OMIM can be downloaded directly from the NCBI FTP site, located at ftp ncbi.nih.gov repository OMIM. Each of the available files is described below. There are no accompanying executables for these files. It is anticipated that users will develop their own front-end applications for using these files, or will use these text-based files for parsing. All of these files are freely available and updated at regular intervals. Complete OMIM text (omim.txt.Z). As the name would...

Basic Protocol 2 Translated Blast Searches

Translated BLAST (Gish and States, 1993) comes in three flavors. In BLASTX, a nucleotide sequence is searched against a protein database. BLASTX is the best tool for finding genes in a genomic sequence or in characterizing a single EST or the assembly of several ESTs that are believed to be reverse-transcribed from the same mRNA. In TBLASTN, a protein query is searched against a nucleotide database translated in six frames. A major use of TBLASTN is finding homologs of an already known protein...

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...

Internet Resources

The NCBI Web site, which offers easy access to OMIM. The FTP site for downloading OMIM for local use. Frequently asked questions (FAQ) about OMIM. From Current Protocols in Bioinformatics Online Copyright 2002 John Wiley & Sons, Inc. All rights reserved. CURRENT PROTOCOLS IN BIOINFORMATICS CHAPTER 1 USING BIOLOGICAL DATABASES UNIT 1.2 Searching Online Mendelian Inheritance in Man (OMIM) for Information for Genetic Loci Involved in Human Disease FIGURE(S) Figure 1.2.1 Search results from a...

Alternate Protocol 1 Finding Repeated Motifs In Protein Sequences

This protocol describes the use of MEME via the MEME Web interface or the command line to discover repeated motifs in a family of protein sequences. It also discusses how to interpret the motifs, compare them with known motifs, use them in sequence homology searches, and construct phylogenetic trees based on them. This protocol is a direct extension of the main method described in this unit (see Basic Protocol 1) where nonrepeating motifs were discovered. It is usually a good idea to extend the...

Review the results

Use a Web browser to view the MEME results. For example, using Netscape Navigator, click on Open Page in the File menu and use Choose File to select the file saved in the previous step (tf4.zoops.html). Then click Open In Navigator. 8. At the top of a MEME output document are six buttons (Fig. 2.4.8). Clicking on these allows one to go directly to the different sections of the MEME output. Just beneath these buttons are three additional buttons that allow the MEME output to be used as input for...

Contributors And Introduction

Research Group for Evolutionary Genetics The Basic Local Alignment Search Tool (BLAST Altschul et al., 1990, 1997) is the most widely used and most productive tool in bioinformatics. BLAST can identify possible homologs in nucleotide and protein databases with high sensitivity and selectivity, and at an amazing speed. Those homologs may provide inference for the biochemical function, exon boundaries, domain architecture, secondary and tertiary structure of the protein, and many other features....

Conduct a MAST search

Fill in the MAST form Fig. 2.4.20 by entering an E-mail address and selecting the S. cerevisiae database. Click on Start Search. MAST will return results by E-mail when they are ready. This may take from a few minutes to a few hours depending on how busy the MAST server is, the number of motifs in the query, and the size of the database being searched. MAST allows searching a large number of sequence databases including all of those available to NCBI BLAST, as well...

Basic Protocol 5 Using Block Maker

Block Maker finds blocks in a group of related protein sequences. Block Maker uses the PROTOMAT algorithm Henikoff and Henikoff, 1991 , a two-step procedure. First, candidate motifs are found using a motif finder. Then, a best set of motifs is assembled along the length of most of the sequences. Block Maker runs PROTOMAT two times, first using MOTIF Smith et al., 1990 and second, using a Gibbs sampler Neuwald et al., 1995 as motif-finding algorithms. It returns both sets of blocks. While the...

Basic Protocol 2 Examining Structures In Entrez

Structure queries can be accomplished simply by selecting Structure from the Search drop-down list on the Entrez Web page. For the example below, assume that the user is trying to find information regarding the structure of HMG-box B from rat, whose PDB accession number is 1HMF. An up-to-date Web browser, such as Netscape Communicator or Internet Explorer 1. Go to the Entrez Web page http www.ncbi.nlm.nih.gov Entrez Fig. 1.3.1 and select Structure from the Search drop-down list. Enter 1hmf in...

Types advantages and disadvantages of network searches

There are several different alternatives to running BLAST searches locally. Servers with Web or E-mail interfaces allow users to fine tune the arguments also called options or parameters , select the database, and launch queries. The strict sense network BLAST application provides a full Unix command-line interface between the user and the remote server. Specialized servers provide another convenient interface to BLAST. For beginners, the National Center for Biotechnology Information's NCBI...

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 Protocol...

Support Protocol Training GlimmerM For A Specific Organism

First of all, a careful, thorough collection of a good training set is a critical first step in the training of any gene finder. The quality of the data used for training is directly proportional to the accuracy of the resulting gene finder. As with any species-specific gene finder, GlimmerM needs to learn about the properties of the genes in an organism before it can find more genes. A good training set should contain as many complete coding sequences as possible from the organism for which a...

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...

Introduction

In April 2003, the biological community will celebrate the completion of the Human Genome Project's major goal, the complete, accurate, and high-quality sequencing of the human genome Collins et al., 1998 . The attainment of this goal, which many have compared to landing a man on the moon, will obviously have a profound effect on how biological and biomedical research will be conducted in the future. The free availability of not just human genome data, but human sequence variation data, model...

Meme

Uet- thii lorn ro i-ubink DNA w piowiii i-t jwits to MEME. MEME mil aaif yz tycvt i latai ts far siffJLsrjits ihttifi Mid jiod tt frupttf for di pantm in Yiurd amp f-s wiL H pw tsstJ on thtIBMfipi-gffflwip'jttr vttlii.i JHfap SwptyoOPf aiwCtarteT .hnd tfeta.- vi-f wJb 5w t by t-Tnsi PU amp s t t rctr dne-i.c-. iiywi bciLcv ilwt ens- oi mont Kttitift. Tfc.t stiyitJKtiiiftdyiirtTiafiiw mwftrliiiiiOjCCO cKwAii-Mrj, ' .-J IT H -y 'Si . HJt 11'i.Tihtr Ijf fajmtjAK. Optiooteslf DttaMM j t i...

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...