There are a lot of genome information for you to browse, and several tools to search genes, expression etc. More details and introduction of this site are available at "About CGRD" page. Meanwhile, the Tutorials of how to use it are on "Tutorials" page. All pages were tested on Chrome browser(Version 41.0), Firefox browser(Version 37) and Safari browser(Version 7.1). The CGRD is not supported well in low version IE browser. You can try above browsers when CGRD does not work well in your own browser.

Tutorials of CGRD


Search information of genome elements from CGRD


Search gene information by identifiers
search-genes-by-id

In the above snapshot, if you want to select several genes' information just by gene identifiers, you can do like this. Select one genome and input gene id list(line by line), if you do not know how to get start, just click "Example" button to load example data, and submit. After the form is submitted, then you will get the follow result.

search-gene-result

There are download button and table of detail information in this snapshot. It just lists the summary information of the selected genes, you can click the ">>more" link to get more information, just like this.

one-gene-table

In the gene page, there are struct coordinates, full function annotation description, transcripts list, homologs list and JBrowse frame of this gene.

Search gene information by genome regrion
search-genes-by-genome-location

You can chose one genome and input the genome region to search genes which are located in this region. The format of the genome region is Chromosome/Scaffold:start position..end position, while the Chromosome name must be recognized by CGRD(Chr01 is no same as chr1 etc.), the start position should be smaller than end position.

Search gene information by Arabidopsis gene ID
search-genes-by-arabidopsis

The proteins in cotton genomes were aligned to the proteins in Arabidopsis genome, so you can input the Arabidopsis gene ID to search the homologous cotton gene. The Arabidopsis gene ID is the normal format in the TAIR website.

Search gene information by function description
search-genes-by-functions

Search the description and symbol field of genes in database by the input text with specific match type(start with, contain, end with).

Search gene information by GO Terms ID
search-genes-by-GOs
search-genes-by-InterPro
search-genes-by-SwissProt
search-genes-by-TrEMBL
search-genes-by-Pathway
search-genes-by-KEGG-Orthology

GO term ID, InterPro term ID, SwissPort term ID, TrEMBL term ID, KEGG Pathway map ID and KEGG Ortholgy ID can be used to search the related cotton genes, while the GO format is GO:XXXXXX, the InterPro format id "IPRXXXXX", the SwissProt and TrEMBL ID is descripted as the UniProt, the KEGG Pathway map ID format is "koxxxxx", the KEGG Orthology ID format is "Kxxxx".

Search Transcription Factors by symbols
search-TFs-by-Symbols
search-TFs-by-Group
search-TFs-result

It is so easy to search Transcription Factors by symbols. The checkbox lists all the available TF symbols. The second image is the summary of the TFs in cotton genomes, while the third image is the result of TF searching.

Search Transposable Elements by identifiers
search_TEs_by_id
search-TEs-result

Just input the list of TE ids like the first image, and you can get the detail information of seached TEs, which includes genome, classification, genome location and strand(second image).

Search Transposable Elements by classification
search-TEs-by-Class

You can search TEs by the classification(LTR, AT_rich etc.) with specific match type(start with, contain, end with). Sometimes, there are too many elements that match the searhing, so part of the result will be displayed, which considers the performence of the website.

Search Transposable Elements by genome regrion
search-TEs-by-Genome-Location

This is the same method like gene search.

Search miRNAs by identifiers
search-miRNAs-by-id
search-miRNAs-result
one-miRNA-table

For miRNA ID search, you can get the information table that contains the description and genome location. The third image displays the full information of the selected miRNA.

Search miRNAs by annotation
search-miRNAs-by-annotation

The annotation of all available miRNAs was obtained from the publication paper, which included the similar known miRNA name and the ID in Rfam.

Search miRNAs by genome regrion
search-miRNAs-by-Genome-Location

This is the same method like gene search.

Search lncRNAs by identifiers
search-lncRNAs-by-id
search-lncRNAs-result

This is the same method like miRNAs search. Note: The lncRNA search is just available in G.barbadense(GCGI 2015).

Search lncRNAs by genome regrion
search-lncRNAs-by-Genome-Location

This is the same method like gene search.

Search information of gene family from CGRD

Search gene family information by member identifier
search-gene-family-by-id
search-gene-family-result

It is available to search the gene family(group) by the member of it, the member can be the cotton gene or the homologous Arabidopsis gene. The result will list all the Arabidopsis genes and all cotton genes respectively.

Search gene family information by Arabidopsis gene ID
search-gene-family-by-arabidopsis
Search gene family information by group ID
search-gene-family-by-group-id

Search and show expression of genes/isoforms by ID list

search-expression-by-id
search-expression-result-table
one-sample-table
search-expression-result-lines
search-expression-result-heatmap
one-sample-table

The expression level of genes/isoforms can be displayed by the input ID list, while the isoform search is just available for G.barbadense(GCGI 2015). The result of searching can be showed as tables, line plot, heatmap plot. The corresponding RNA-seq samples are also available.

Query sequence in CGRD with aligners

Query sequence with BLAST
doblast
doblast-result

In the sequence alignment(BLAST) section, the basic form of blast is provided, which contains the sequnece input box, alignment program, alignment database and the e-value cutoff etc. The input sequence must be the fasta format, in other word, your input sequence must have the header line that contains the ID. The web blast aligner in CGRD just accepts one sequence. The result panel will show the parameters of this alignment ans the output of blast(-m 8), meannwhile, the detail alignment can be showed as graphic, the basic color is red, and the transparency is refered to the identify of the corresponding alignment.

Query sequence with BLAT
doblat
doblat-result

In the sequence alignment(BLAT) section, CGRD provides all the cotton genome sequences, gene sequnece as the target database, the NT vs NT is accepted in CGRD BLAT alignment. The content in the output panel is similar as the BLAST panel, while the color will be red when the alignment is "+" strand, the color will be green when the alignment is "-" strand.

Search all pairs in gene collinearity blocks

search-gene-collinearity-by-id
search-gene-collinearity-result
view-gene-collinearity-by-chr
search-gene-collinearity-result

Like the gene family search, the gene collinearity block can be search by the member ID. The output panel displays the content of gene collinearity block as table. In this table, one line is treated as one pair of block. Futhermore, you can also view the block by the chromosome in specific cotton genome(reference), where tandems are marked in red.

Search synteny blocks by genome region

search-synteny-block-by-genome-region

The genome region is the text in the "Landmark" text field, the genome you want to search is the checkbox element in "Genome to Search", the aligned species can be checked in the "Aligened Species". The detail panel shows the detail synteny blocks of your choice.

View KEGG Pathway maps by cotton genomes

view-pathway-by-map-genome
view-pathway-by-map-genome-result

All the proteins in cotton genomes were aligned to the KEGG Orthology, so the proteins are associated with the emelemts in KEGG Pathway map. The pathways wera listed in one page with liks to the specific map. In the map image, the colored rectangle or line are the elements that the cotton proteins are associated. Put the mouse on the elements or just click it, then you will get a window that contains the associated genes and its symbols. The gene name in the table can be clicked to the detail page.

Get and browse data in CGRD

Bath sequence retrieval by ID list
batch-sequence-retrieval
batch-sequence-retrieval-result
batch-sequence-retrieval-result

In CGRD, you can get some sequences by their IDs. The CGRD gets the ID input and uses the fastacmd command in BLAST package to extract the sequences in database. The result panel will display the links of sequnecs and error log.

Browse genome data with GBrowse
gbrowse-homepage
gbrowse-select-tracks

The GBrowse(GMOD project) is a good tool to view the gene model, RNA-seq alignment etc. of genome. In CGRD, all the data of cotton genomes were uploaded to the GBrowse. You can select tracks what you want to see, take a snapshot of the specific genome region with selected tracks.

Browse genome data with JBrowse
jbrowse-homepage
jbrowse-homepage-extract-fasta

The JBrowse(GMOD project) is a similar tool of GBrowse to view the gene model, RNA-seq alignment etc. of genome. It has different UI with GBrowse, but the similar funtions with GBrowse. In genearl, the tracks panel and the details panel in the same windows. In the left track panel, you can chose which trak to be showed in the right detail panel. In the right detail panel, the tracks were listed one by one, they can be dragged to change the order. The popmenu is useful to get the detail of this track. In the top-left corner of right detail panel, you can switch which genome to view just by clicking the item in the checkbox. If you want to see the detail of some element in one track, just click it, and you can get some data like fasta format sequence or GFF3 format annotation file.

Bulk download with FTP server
ftp-sever

In the FTP server of CGRD, you can download all available cotton genome data, which includes the annotation files, sequences files and the indexes files processed by bowtie2 and bwa aligners.

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