RiceGE: SIGnAL Rice iSect Tools ( Oct. 6, 2010 )

• 1. Preferences : Edit your preference to set your own values of the image width, the zoom factor, UTR regions and promoter, to hide or show a set of data, as well as to change display shapes, sizes, colors and track spans instead of default settings. It has less priority than the iView Tool.

• 2. Search : To open a browser window by querying a gene, a BAC, or data (cDNA, T-DNA) and function. For example: psbA or PFG_3D-00625.R.

• 3. Locate : To open browser window by positiohing its location (chromosome and position).

• 4. Fetch : To retrieve all displayed data from a chromosome region. For example: 1234-2345 or W/1234-2345.

• 5. mText : It is now evolved to accept multiple search for both gene list or cDNA/T-DNA/other list to retrieve related or hited data or genes. For example:

  	please choose type: Gene for gene list or Data for cDNA/T-DNA list.
  
  	psbA
  	nad2
  
  	or
  
  	PFG_3D-00625.R
  	PFG_2A-10162.L

• 6. iSectR : iSect (R) tool to retrieve sequence from a specific chromosome region. For example : 1234-2345 or 1234-2345,3456-4567.

• 7. iSectL : iSect (L) tool to retrieve sequences from genome by list of data names or list of genome mapping data. For example:

  	psbA
  	PFG_3D-00625.R
  	PFG_2A-10162.L
  
  	or
  
  	query1 chloroplast 0.0 W/1234-2345
  	search2 chr01 0.0 C/1234-2345,3456-4567
  

• 8. PrimerL : iSect primer (L) tool to design primers according to a list of data names existed or a list of genome mapping data. For example:

  	psbA
  	PFG_3D-00625.R
  	PFG_2A-10162.L
  
  	or
  
  	query1 chloroplast 0.0 W/1234-2345
  	search2 chr01 0.0 C/1234-2345,3456-4567
  

• 9. PrimerS : iSect primer (S) tool to design primers from user input sequences. For example:

  	>YourInput.fa
  	CTCGCTGGCCTGTTCAGGTGAATCTTAGTATCGTTTTGTGTCCATGTTGCCTCTACTTCG
  	CCTGCTTCTGGTGACTTGAATTCTCTCTTTGTTTTGGGCAGCTTCGGGAACCTTCCACAT
  	CCGAAGATGCTGAATTCGCTTCTATTTTGCGGACTCTCAAGGACAGTTTTGATAACGCAT
  	TCACTGCTATGATTTCCTTCCAGACGAAGAATTCCGAGCGCATATTCAGCACAGGTATAA
  
  
  10. GeneAtlas : Gene express atlas query tool by probe name or gene name. For example:
  	Qurey:  AFFX-BioB-3_at NULL  001-200-E04 Os07g04850 
  	Filter:  GSE7951:stigma ABA treated
  	Custom Data: 257 21 567 24 [Signal Stdev ... ]
  	Custom Label: My_data_1 Your_data_1 Thee_data_4 ...