Rev.4, 29/Jun/2010	

How to use “KAIKOGAAS” on the web	

KAIKOGAAS consists of 5 main pages: the top page, Scaffold-Chromosome (scaffold) table page, BAC table page, On-line users page and the Annotation
Map page. The top page contains links to scaffold annotation table, BAC clone annotation table, and submission page for on-line users. Annotation of 192
scaffolds mapped on the 28 chromosomes could be accessed by clicking the corresponding chromosome number. Additionally, annotation of 4,615 unmapped
scaffolds are available in chr_Un. The annotation of BAC clones could be accessed through the BAC clone Table link. The results of on-line submission canbe viewed through links from the on-line analysis page. The Annotation Results page shows an annotation map with the automatically predicted gene sets. 	

Fig. 1 The 5 main pages of KAIKOGAAS. 	

1	

Fig. 2 presents an example of KAKOGAAS result for scaffolds on chromosome 1. KAIKOGAAS has a limitation in size up 200 kb for processing data,
therefore, large scaffolds having more than 200 kb are divided into 200 kb pieces, which are labeled with “Scaffold segment ID”. The link to “KAIKObase”
provides view to scaffold position on chromosome and transcriptome information, etc. For details, please visit KAIKObase homepage. 	

Scaffold in “Clone name” column is described in orderon chromosome.	

Clicking the Accession No. opens the details of the clone
sequence as registered in DDBJ.	

Clicking KAIKObase jump to KAIKObase of keyword
result page, user can be viewed scaffold position on
chromosome and transcriptome information so on. 	

Clicking the Divided Name opens the annotation map.
See Fig. 3.	

Begin, End of Scaffold segment ID positions byreference to scaffold and length of Scaffold segment
ID.	

Scaffold length wit gap.	

Fig. 2. scaffold build2 table 	2	The annotation map page consists of three sections.	

The upper frame shows a graphical representation of the results of the 	different prediction programs, homology searches and predicted gene models.	

See Fig. 4.	

The middle frame allows the user to specify the start and/or end base point	

of the map viewer and change the magnification (x1-x5). Clicking the“Redraw” 	

button executes the changes. Clicking the blue arrows adjusts the map viewer 	to the 0 bp position, full-screen scroll, half-screen scroll ,	or scroll to the end of clone/scafflold segment ID.	

The lower frame provides an option for selecting or clearing	

specific data in the annotation map by checking or clearing 	the boxes provided for each analysis program. Clicking the“Redraw” 	

button executes the changes in the annotation map.	

Fig. 3 Annotation Results Page	3	

Clicking any region of the autopredgeneset or predgeneset (BAC clone 3L13, 4L14 only)	

(green bar) shows the detailed information of the predicted gene model. See Fig. 5.	

Clicking any region of the gene predicted by any prediction program (bluebar) shows the detailed information of the predicted gene. 	

Clicking any region of the protein or EST homology shows the detailed 	

results of Blastx (orange bar) or Blastn (red bar). 	

Fig. 4 Details of annotation map	4	

Result of domain search against Pfam database.	

Detailed information of the predicted gene including chromosome	

number, clone name, position of exons and GC content.	

Results of homology search using Blastn (top 3 ESTs),
Blastp (top 10 proteins), HMMER and ProfileScan with thecorresponding alignments of the sequence.	

Display the results of queries to amino acid analysis	sever/site such as PSORT, SOSUI and MOTIF.	

Links to the nucleotide sequence, spliced nucleotide sequence	and translated protein sequence of the predicted gene.	

Fig. 5 Details of predicted gene model	
5	

Fig. 6 Autopredgeneset summary page	

Clicking the clone name opens the annotation of this contig. See Fig. 3. 	

The summary list page	

Clicking here opens the details of predicted gene model. See Fig. 5.	

6	Fig. 7 On-line annotation of sequence data	On-line users can submit sequence data for annotation after registering an e-mail address and password from on-line	

users top page. After being authenticated, the sequence can be submitted directly. The results can be viewed after one	day through the data list page.

Registration page	

On-line user top page	

Data entry page	

Authentication page	
Userʼs page	7	

List of annotated sequence