This page describes the information provided for each of the PEDE assemblies. Each nucleotide sequence, the cluster to which it belongs, its genomic structure as suggested by comparison with the human genome sequence, representative RefSeq and UniGene BLAST results, SNP locations, and an alignment of the reads comprising each assembly are shown.
Sequences of the contig or singlet in the PEDE assemblies can be obtained in FASTA format. On the singlet page, regions of low-quality sequence data are indicated in gray letters (on the main pages) or in lowercase (on the FASTA format pages).
Information on the specified assembly - such as length, aligned reads, SNPs, and estimated genomic structure - is shown schematically.
(Upper) Sequence information matched to the human genome sequences can be obtained by clicking the aligned red arrows. Results of BLAST searches against the draft sequence of the human genome can be inspected through the link indicated by the human chromosome name.
(Lower) Aligned reads to the assembly (contig). Read(s) shown in red indicate the clone(s) that have been finished sequencing. Detailed information of the finished clone can be obtained by clicking the name of the read shown in red.
Results of BLAST searches using the specified assembly as a query against the human, mouse, dog, cattle and pig RefSeq protein sequences are summarized. Results with low scores (< 50) are shown if results with higher scores do not exist. Links to the GenBank pages and raw BLAST results are provided. The probability that the assembly includes a full-length CDS is indicated..
Results of BLAST searches using the specified assembly as a query against the human, mouse, cattle, and swine UniGene nucleotide clusters are summarized. Links to the GenBank pages and raw BLAST results are prepared. The probability that the assembly includes a full-length CDS is indicated.
EST reads belonging to the specified assembly are listed. Sequences of the reads can be obtained through the links. Detailed information and sequences registered in GenBank of cDNA clone(s) that have been finished sequencing can be obtained by following the indicated links.
Information on the putative SNP(s) in the specified assembly is summarized. Only alleles detected with high reliability (PolyPhred rank < 3) in other breeds are counted in this table. "Type" is as follows:
W: Detected only in western breeds. M: Detected only in Meishan breed. B: Detected between western and Meishan breeds. O: Other (detected in both western and Meishan breeds).
"AA Change" refers to the effect of the SNP on the coding amino acid.
N: Non-synonymous. The SNP is thought to change the coding amino acid. S: Synonymous. The SNP is not thought to change the coding amino acid. -: Cannot be determined. Influence of the SNP cannot be determined because the reading frame cannot be estimated.
Alignment of the EST reads to the contig sequence. Locations of the SNPs are indicated by colored letters.
We estimated the assemblies as encoding full-length CDSs if the length upstream of the matches (BLAST score > 50) in the EST assemblies were longer than the length between the start base of the CDSs and the matched region of the corresponding genes.