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Annotations and Definitions
Annotations and Definitions
Genome alignment
Genome mapping
For mapping of cDNAs to genomes, a program to map the cDNA sequence onto the genome.
GO term assingment
Identification of CpG-like element
For the analysis of CpG islands, the moving average for %(G+C) and the CpG ratio were calculated for each sequence, using a 100-bp window moving along the sequence at 1 bp intervals. The CpG ratio was calculated according to the standard method (Gardiner-Garden and Frommer, 1987): (number of CG x N) / (number of C x number of G), where N is the total number of nucleotides in the sequence being analyzed. CpG islands were defined as regions larger than 200 bp with %(G+C) > 50 % and CpG ration > 0.6.
Search region is -1000 to +200 (TSS is designated as 0).
Identification of putative orthologous (counterpart) genes
Putative orthologous (counterpart) genes were correlated between species by TBLASTN using their encoded amino acid sequences. In the current version, all of the sequences are mapped onto P. falciparum genome, because it is most complete.
Identification of SSSP
Promoter region -1000 to +200 (TSS is designated as 0) was searched for pattern of "AAGGAATA".
Motif search
RefFull
Ref-Fulls were generated as a hybrid with the annotated genic sequence with the physically isolated cDNA sequence using BASLTN.
Subcellular localization prediction
For subcellular localization prediction, a prediction program, PSORT was used.
Its home page is at http://psort.hgc.jp/
TATA box
-TATA(pattern): Searched for TATA[T/A][T/A] from promoter region corresponding to -90 to +27 (TSS is designated as 0).
-TATA(V$TATA_C): TRANSFAC position weight matrix search (Match)(matrix: V$TATA_C, search region: -90 to +27 (TSS as 0), core sim.: 0.77, mat. sim: 0.77).
-TATA(V$TATA_01): TRANSFAC position weight matrix search (Match)(matrix: V$TATA_01, search region: -90 to +27 (TSS as 0), core sim.: 0.77, mat. sim: 0.77).
-TATA(TATA_Pf): Searched for T[A/G]TAA from promoter regin corresponding to -1000 to +200 (TSS is designated as 0).
Transmembrane domain prediction
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