1.How to use this database?
There are 7 different content pages included in this database: Home, short introduction of the litchi genome project; Mapview, genome browser to show detailed annotation information for each genomic region; Blast, sequence homology searching service against the litchi genome, CDS and protein from predicted genes; Download, data access via ftp; Help, equal to FAQ, answers to the main questions; Links, some related bioinformatic tools; Contact, contact information. You will get support by the help information on each page. If any further question, please feel free to contact us.
2.How to search gene?
After login, you can search a gene via search box on homepage. First, select “gene”, input a gene id, for example “Litchi_GLEAN_10034169”, then click on the “GO” button. And you will get the result. You can click on the gene name to view detailed information and click on “Map View” for the gene map.
3.How to use the genome browser Mapview?
1) Click on “Litchi_k69” on the left of the mapview interface and select a reference sequence to browse.
2) Click on “Features” in toolbar and select a feature. You can browse Genes, Repeats, ncRNA, InDel, SNP, SV with their tracks. Some information of a feature can be viewed with cursor on it. For more information of the feature, just click on it. You can view GC percent of the reference sequence via GC% track, and view actual sequence via Reference track. Click on “Position” in toolbar and specify a position to start browsing.
3) To specify a region to browse, click on the “Region” button.
4) You can use “+” button to zoom in and “-” button to zoom out. If the zoom is set to 100bp, the actual sequence of the genomic scaffold can be viewed.
5) You can specify a gene or scaffold to browse via the search box.
4.How to run BLAST?
1) Select a program and a database. There are eight BLAST database. More information about the BLAST database, please click “Database”.
2) Enter a sequence in FASTA format in the input box.
3) Click on “Search” button to run BLAST. You may set some parameters before running if needed.