How to get BAC/Fosmid clones harboring your gene.

We can identify the BAC/Fosmid clones harboring gene of interest using UTGB/medaka and ensembl.

1. By UTGB/medaka

1. Paste your sequence on the online mapping window in UTBG/medaka and push search.

2. You can see the view like Figures 1(3) and 3(2).  Note the clone names in BAC end track and Fosmid end track.

3. Send the clone name with the mailing information to NBRP medaka ( mbrc@nibb.ac.jp ).

2. By Ensembl

1. Go to Ensemble Blast view ( http://www.ensembl.org/Oryzias_latipes/blastview ).

2. Paste your sequence, push RUN and retrieve result.You can see the result such as Figure 2.

3. Go to contig view and select “View region in Medaka genome browser”(Figure 3(1)). You can see the exactly the same region in UTGB/medaka and note the clone name in BAC end track and Fosmid end track (see also Figure 3(2)).

4. Send the clone name with the mailing information to NBRP medaka ( mbrc@nibb.ac.jp ).


Figure 1

Figure 2

Figure 3

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