Web-based tools for Bioinformatics; A (free) introduction to (freely available) NCBI, MUSC and Worldwide.

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1 Page 1 of 32 Web-based tools for Bioinformatics; A (free) introduction to (freely available) NCBI, MUSC and Worldwide. When and Where---Wednesdays 1-2pm Room 438 Library Admin Building Beginning September 10, Overview NON-human Genome Resources November 19, 2003 Introduction/Scope The short answer is that there are a LOT of projects out there. The technology that sequenced the human genome is still out there and now it's being harnessed to examine the next series of useful genomes. The agricultural species of plant and animal are being worked on as are the pathogens and parasites with global impact. There is considerable scientific as well as political discourse about the projects to be pursued and the order of their pursuit. Here is a casual listing of Genome pages/projects. The main thing you notice as you click through just this partial listing is that there is a HUGE variability in the progress and access to data. NCBI and ENSEMBL are far and away the best integrated sites for analysis via the web. The vast majority of non-bacterial genomes have only a limited coverage of their respective genomes and this annoying fact of life is just something you have to deal with. The encouraging thing is that with a wide array of open source software out there, you can without reinventing the wheel too much, adapt software to your own project. Nematode NCBI, ENSEMBLelegans, ENSEMBLbriggsae,WormBase FruitFly NCBI, ENSEMBL, Flybase, UCBerkeley Malaria NCBI, UWisc Dictyostelium DictyBase, DictyGenome Microbes NCBI, TIGR, ORNL Mosquito NCBI, ENSEMBL, Colo.State Mouse NCBI, ENSEMBL,MGI,NIA/NIH, ORNL Rat NCBI, ENSEMBL,RatMap Zebrafish NCBI, ENSEMBL, ZFIN Retroviruses NCBI, Vial Genomes NCBI Parasite ParasiteGenome,TIGR Yeast SGD

2 Page 2 of 32 Plants NCBI, ArabidopsisUK, RiceJapan, MedicagoOU, USDA List, USDA Wheat, USDA Wheat Data Chlamydomonas OklahomaU, Fugu ENSEMBL, MRC, JGI GenomeChannel ORNL Meat Animal Research Center USDA Cattle Sheep Swine Genome TIGR Eukaryotes Organelle Genomes NCBI Your favorite bacterium revealed [T] - TaxTable; [P] - ProtTable; [C] - COG Table; [D] - 3-D neighbors; [L] - BLAST; [S] - CDD search [F] - FTP Examples for E coli K12 T Taxonomic distribution P Gene by gene Table of Genes C COG summary D Proteins with known structure L BLAST Query page for that genome S Structure Conserved Domains F Download as FASTA format the whole genome

3 Page 3 of 32 BLASTING some or all the microbial genomes. PDB neighbors for bacterial proteins Bacterial genome sequencing projects listing A logical question to ask is how similar are two species. The NCBI TAXPLOT tool is designed to help visualize an answer to this problem. Homologene You can download all of the Homologene content COG/KOG Tool New. Clusters of classified organisms Old COG page COG Help Virus Resources Naming/Taxonomy Conventions What is a virus? Influenza Virus Replication Summary. Viral genome statistics. Viruses by Taxonomic Group BLAST versus Viral genomes. Related viral proteins Virus COGs = VOGS. A worked Example Let's go to the Homologene page and search for CASP7

4 Page 4 of 32 This gives us a few hits

5 Page 5 of 32 Some more of the CASP7 Homolgene entry

6 Page 6 of 32 Let's try a similar search via the COG/KOG tool

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8 Page 8 of 32 From this page we can select KOGNITOR and perform a BLAST search against the KOG database. Here is the link to the CASP7 sequence

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11 Page 11 of 32 Clicking on KOG3573 shows the taxonomic distribution of the hits. Note there are no yeast,or plant COG hits.

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13 Page 13 of 32 One level further shows

14 Page 14 of 32 Pathways in COG

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16 Page 16 of 32 Phylogenetic page allows you to perform some interesting selection procedures. For example suppose you were looking for potential drug targets in gram positive bacteria which would have no effect on humans. You might start by using this tool. In the interactive page you see three icons in each cell of the table. These represent the applied selection criteria. The Green orb is a check meaning must be present. The red x means must be absent. The yellow orb means you do not care. The reset button is in the upper left. In the image below the yellow orb in the size cell is checked and 66 COGs are indicated. These show 13 in Archaea, 12 in Grampos and 7 in alpha for instance. Clicking the "show" button displays all 66.

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18 Page 18 of 32 Here is the same Phylogenetic window set up this time select COGs which exist in grampos bacteria (12) but are absent in eukaryotes (3 with red x) and the rest are marked as neutral (yellow orb).

19 Page 19 of 32 The Show button displays 70 COGs which fit the selection criteria. Note that the authors

20 Page 20 of 32 have elected to display results with two similar pastel color schemes that actually represent two distinct features. On the left of the image below the colors map to broad groupings of species Species colors Gene Function Colors, whereas on the right the colors code for functional categories. This is not helpful to the viewer to say the least. Below are the 70 COGs. Again the left pastels are organisms the right pastels are functional groups.

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22 Page 22 of 32 From this set of 70 COGs you might for instance seek a target for penicillin. This is wonderful bioinformatics but what if the drug is hyperallergenic? If you examine one of the COGs eg COG0195 you see. The minuses in the pink bar highlighted at the top correspond to the eukaryota section where no entries have been selected. The yellow bar at the top represents the Archaea with 13 entries. In the phylogram on the right the 13 yellow diamonds correspond to the 13 Archaea COGs that have been selected. Off the view at the bottom of this screen shot are 12 grampos entries. If the full tree were visible you could count the 12 light blue grampos COGs. The tree is not linked but the left hand table entries are linked to archived COG/BLAST searches

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24 Page 24 of 32 Using TAXPLOT is interesting as a nifty comparison tool.

25 Page 25 of 32 You can select species and then either genes or function and you will see: Here is a result comparing three species of bacteria and selecting ion transport

26 Page 26 of 32 proteins. You can see the matches and you can see the BLink to the lower right.

27 Page 27 of 32 Looking up SARS virus example Start at the VIRUS homepage and enter SARS

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29 Page 29 of 32 Click on the Complete Genome Link

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31 Page 31 of 32 Starting with ENTREZ search for Influenza A virus Retrovirus Genomes Retrovirus BLAST to identify genoptype. Align a sequence to retroviral genomes Specific pages for retroviruses

32 Page 32 of 32 HIV1 HIV2 SIV HTLV STLV Country distribution of HIV-1 Sample Questions/Data Use the COG phylogenetic table to find targets for drugs in Gram positive bacteria. These would need to be essential for grampos bacteria but absent from archea for instance. See if you can locate any sequences from the 1918 influenza epidemic. What type Virus is the PARVOVIRUS? 7 clones of the same isolate of HIV-2 subtype A have been partially sequenced. All of them are from a German woman infected via heterosexual contact with a Senegalese man in The woman has since died of AIDS. Both the woman, and the Senegalese man had AIDS at the time blood samples were collected. Human immunodeficiency virus type 2 (HIV-2) has been sequenced (complete proviral genome, Accn. M30502; this sequence is also an isolate from Germany, but the person probably got infected in Mali). How many differences in the sequence are approximately found for each of the 7 isolates in the envelope glycoprotein (env) gene? This is an alignment problem. Created by ESH ; updated :30 to Starr about this page