useful+sites

Posted here are sites used by students in Dr. Kenick's genomics course that they have found helpful. They have the actual address as well as a brief description of the site/tool found there.

Julienne Kapelson

1) [|Entrez] the Entrez cross-database search allows you to search any type of life sciences query, whether pertaining to genes, chemistry, biology, etc., and lets you define your search to gain the most useful information possible on any given query.

2) [|MapViewer] MapViewer allows you to search different genes and proteins and shows where the particular protein is located and in which chromosome in detail.

3) [|GeneNames] Database that allows you to search through over 28,000 approved gene symbols to find out more about that gene.

4) [|Yeast Genome] Database of molecular biology that is focused towards the yeast Saccharomyces cerevisiae. It allows you to more completely understand the yeast genome.

Stacia Stickney

1) BLAST- Basic Local Alignment Search Tool http://blast.ncbi.nlm.nih.gov/Blast.cgi Database that allows you to find regions of local similarities between sequences. You can compare nucleotide sequences or protein sequences to database information to see the statistical significance of the matches. We used BLAST to figure out gene families, find e-values and bit scores, amino acid sequencing, compare nucleotide bases with e-values, figure out what mystery sequences may be, figure out what a protein may be and what organism it comes from, and much more.

2) GeneCard http://www.genecards.org/ Database that allows you to search for different gene symbols and gives you descriptions of different genes. This site is full of human genes and gives you genomic, proteomic, transcriptomic, genetic, and functional information on all known genes. We used GeneCard when we were given the symbol of a gene to help figure out what the gene was as well as its function, as well as to learn more about different Genes and their roles.

3) GeneXplorer http://genome-www.stanford.edu/breast_cancer/molecularportraits/explore.shtml A database that allows you to search through a large amount of information on DNA micro-array experiments. We used GeneXplorer to focus in on specific genes in a DNA micro-array and learn more about their functions.

4) CMR- Comprehensive Microbial Resource http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi This website is used to display the information of complete prokaryote genomes. Cross-genome analysis also helps to compare the genomes to one another, highlighting similarities as well as differences among the organisms. We used CMR- Comprehensive Microbial Resource, to learn more about the organism //Bucherna//. We saw its relationship with //Aphids// and were able to see the entire genome for //Bucherna//.

1.**Genemark** [] This is a great way to look at gene location on chromosomes in an easy to understand format. I used it to compare human and mouse chromosomes. It is a gene prediction program.
 * Nancy Fernandes**

2. **ECR Browser** [] This site ensures a very cool graphic of evolutionary synteny between species. It is easy to navigate and you can use the little pictures of your species on a phylogenetic tree!

3. **Ingenuity Pathways Analysis** [] You can download this program for free for 14 days. I used it to create a intergenic pathway of gene cascade and added function and disease. There are many graphics to choose from and it is connected to just about every bioinformatic tool I know of. There is also a sort of literature tool to look up information on, similar to PUBMED.

4. **Geneious** [] It works just like it is named, //Geneious//. This is an essential tool to create alignments for phylogenetic trees. It also saves all of your searches and information in one convenient location.

Robin E. Renzi 1. **Protein Data Bank** [] This site allows for the viewing of exterimentally-determined quaternary structures of proteins and the identification of mutations within the proteins.

2. **Canine Genome** [] This site shows how a boxer's DNA was sequenced and used to discover canine genes that are universal across all canines and their disease implications.

3. **Tree of Life** [] This site allows for the viewing of gene lineages and also how these genes exist in multiple species such as homologues and orthologues.

4. **First Glance** [] This site is a visualization tool that allows for macromolecular viewing.


 * Alexandra Scott**


 * 1.** Ensembl- [] : a genomic database browser that provides information concerning locations of genes along chromosomes.


 * 2.** NCBI's Protein- [] : a searchable database for protein sequences including translations from annotated coding regions in GenBank.


 * 3.** UniProt- [] : database that is searchable for protein sequences and displays all related information concerning function.


 * 4.** GeneCard- [] : a search engine for human genes that has compiled information from various sources and integrated them to give detailed information about each gene and it's function

Duyen Ha

1. ELSI- [] (Ethical, Legal,Social Issues) allow you to research anything related to ethical, legal, and social problem involving genetic.

2. PLoS Biology- [] allow you to acess through various journals and articles that deal with amazing scientific exploration.

3.Gene Ontology- [] a database which provide informations based on genes and proteins.

4.NCI- [] (National Cancer Institute) can be used to search for informations that are cancer related.

Jared Thistle's awesomely helpful links (not in order of any kind, not by awesomeness or usefulness)

1. OMIM- [] This site was great for gathering basic information as well as providing real-world documentation of the genetic disorders we've studied.

2. BLASTn- [] was useful for analyzing all kinds of sequences. The other sites on the blast page were also useful.

3. KEGG pathway- [] One of my least favorite things in biology is keeping track of all the pathways and how they flow, this site makes it easy.

4. Genecards- [] incredibly useful for general genetic knowledge, this site was incredibly helpful in nailing down the basics and locations of many genes.

Dhurata Baci

1) Genescan-( http://genes.mit.edu/GENSCAN.html) this program is used for predicting the locations and exon-intron structures of genes in genomic sequences from many types of organisms.

2) Unigene- (http://www.ncbi.nlm.nih.gov/unigene) is a database that contains transcript sequences that seem to come from the same gene, as well as information on protein similarities, gene expression, cDNA, and genomic location.

3) SGD- http://www.yeastgenome.org/ (Saccharomyces Genome Database)- contains the molecular biology and genetics of the yeast Saccharomyces cerevisiae.

4) DIP- http://dip.doe-mbi.ucla.edu/dip/Main.cgi (Database of Interacting Proteins)- contains information about protein-protein interaction.