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Tools Tutorials

For a link to each resource click on its title or icon, except for 'Find SNP and INDEL Variants' and 'Retrieve Gene Sequences'. These resources/use cases contain multiple links to access the associated tools.

Apollo Is an instantaneous, collaborative, genome annotation editor. Apollo is designed to support geographically dispersed researchers.	Biomart Use for big and small scale data mining queries that are not as easy or even possible to do using Search/Advanced Search.
BLAST Finds regions of local similarity between sequences. Contigs, scaffolds, chromosomes and in silico (transcripts, peptides) and in vivo (RNAseq, mass spectrometry) data sets are avaialble.	ClustalW Is a sequence alignment tool. Can be used to generate input files for HMMER. After running a job just click on the link "Send to HMMER".
Comparative Genomics Browse for precomputed displays of protein and DNA comparisons, for all and selected genomes, respectively.	Expression (in the Genome Browser) It has microarrays and RNA-Seq experiments with and without differential expression, aligned against genomes. Query the data using the Expression Browser or Search/Advanced Search.
Expression Browser and Map It has microarray and RNAseq data from different experiments showing differential expression. Data is processed through the same pipeline so that results can be compared side-by-side.	Find a Data Display Choose a gene, region or variant and then browse for relevant visualizations that include many different types of figures and tables.
Find SNP and INDEL Variants Variant information shows figures and tables with the variant ID, location, alleles, class, source, consequence type, resulting aa and SIFT score. Access the data using the Advanced search or the Find a Data Display tools.	Galaxy Galaxy is an open, web-based platform for data intensive biomedical research.
Genome Browser Makes genomic data accessible. Data is not only the genome sequence itself, but also other features such as comparisons between species including in silico and experimental data.	HMMER It looks for homologous genes, but unlike BLAST it aims to be more accurate and better to detect remote homologs. Input file is a protein multiple sequence alignment (MSA) from ClustalW.
Ontology Browser Ontologies are the structural framework for organizing information and are used in the Expression Browser and PopBio. You can also use them to annotate the metadata of your research.	Population Biology (PopBio) Use it for visualization, search and analysis of a wide range of population data, including genotypes, insecticide resistance and other phenotypes, and field collection metadata.
REST API Direct programmatic access to VectorBase species data.	Retrieve Gene Sequences For single or few genes use the Genome Browser (ntd and aa). For multiple genes use Search/Advanced Search and BioMart. For whole genomes use BioMart or the Download files.
Sample Explorer Search and explore metadata associated with biological samples and display them in the Genome Browser and PopBio.	Use My Own Data in the Genome Browser Different file types can be upload and visualized along the genome like other tracks.
Variant Effect Predictor (VEP) Determines the effect of variants (SNPs, INDELs, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. The input needs the coordinates and the nucleotide changes of the variants.