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Manual for Sinbase
# Main page
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  • Home: quick navigation; management; search Sinbase; instruction for S. indicum genome sequencing project; news in Sinbase; how to cite; hot link and journals links.

  • Browse: phenotypes; genome composition (including: putative gene sets, repeat elements, non-coding RNA); genetic linkage map; comparative genomics (including: synteny regions among A. thaliana, G. max, S.lycopersicum, V.vinifera and S. indicum; genome browser by scaffolds and pseudomolecular chromosomes.

  • Search: general search (query: gene ID, repeat element ID, non-coding RNA ID); orthologous genes; colinear regions among species; advanced (local BLAST)

  • Document: data statistics (data statistics of Sinbase collected); references (references about S. indicum genome.); resources links (useful links).

  • Help: manual (manual of using Sinbase); feedback (send your suggestions or advices to administrator).

  • Download: download (data files of Sinbase).

# Genome component page
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User can browse genome components of S. indicum, including putative genes, repeat elements and non-coding RNA by popup manu and also can click cartoon picture of pseudochromosome to get information of corresponding pseudochromosome. For putative gene, there are 3 parts in this section, gene basic information, putative function and sequences.

# Linkage page
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User can browse the genetics linkage group of S. indicum by clicking the tab. From each cartoon picture of genetics linkage group, users can get information of genetics linkage group and corresponding markers which can be used to anchor scaffolds from S. indicum genome. 

# colinear regions page
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This is an colinear regions example between S. indicum and A. thaliana genome.  In this page, colinear regions with different length were distinguished by different colors. Through clicking pseudomolecular chormosome ID, user can browse colinear regions  between target chromosome and corresponding species.


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This is an colinear regions example between A. thaliana  Chr01 chromosome and S. indicum genome. Users can retain that there are 97 colinear regions between  A.thaliana  Chr01 chromosome and S. indicum genome.


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Picking up a region of A. thaliana Chr1 chromosome as an example, users can browse details of target regions compared to S. indicum genome. Further, users can get gene pairs between the two regions.


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