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Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile

Data description
Data name
Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile
DOI
10.18908/lsdba.nbdc00419-002
Description of data contents
Contig sequences of cDNA sequences of Dictyostelium discoideum and their annotation (amino acid sequence and results of homology search (with target DBs: contig sequence-DB, DNA-DB and protein-DB)). Contig sequences are obtained by assemblying 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence by the assembly program Phrap (<a href="http://www.phrap.org/index.html">http://www.phrap.org/index.html</a>). Link to the list of clones constituting the contig, the information on its mapping to the genome mapped to genome sequence and the list of top 10 hits in the results of homology search are provided. Also, the number of clones constituting the contig in each library is given for five developmental stages and 14 different libraries. Library-specific clones can be searched. The data are given in a CSV format text file.
Data file
File name :
dicty_cdb_contig.zip
File URL :
File size :
91.6MB
Simple search URL
http://togodb.biosciencedbc.jp/togodb/view/dicty_cdb_contig#en
Data acquisition method

-
Data analysis method

EST sequences were assembled by Phrap.
Number of data entries

8,402 entries
Data detail
Data item Description
Contig information

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Contig ID

ID of contig sequence
Contig update

Last update of sequence
Contig sequence

Contig sequence
Gap

Presence of gap (-) in contig. -If gap is included: gap included. -If gap is not included: no gap.
Contig length

Length of contig
Chromosome number (1..6, M)

Chromosome number of the chromosome to which the contig is mapped. If mapped, numbers 1 to 6 or M (mitochondria) will be used.
Chromosome length

Length of the chromosome to which the contig is mapped.
Start point

Start position of the contig mapped to the genome.
End point

End position of the contig mapped to the genome.
Strand (PLUS/MINUS)

Direction of the contig mapped to the genome (PLUS/MINUS)
Number of clones

Number of clones constituting the contig
Number of EST

Number of ESTs constituting the contig
Link to clone list

Link of all clones constituting contig to TogoDB edition. Link to the clone list is provided in the TogoDB edition only.
List of clone(s)

List of clones constituting contig. Link to each clone is provided in the TogoDB edition only.
Annotation

-
Translated Amino Acid sequence

Representative amino acid sequence translated from DNA sequence.
Translated Amino Acid sequence (All Frames)

Amino acid sequences resulting from translation in all six reading frames of DNA sequence.
own update

Last update of blastn search against contig sequences in dicty_cDB.
Homology vs CSM-cDNA

List of top 10 hits in blastn search against contig sequences in dicty_cDB.
dna update

Last update of blastn search against DNA sequences in public database.
Homology vs DNA

List of top 10 hits in the results of blastn search against DNA sequences in public database.
protein update

Last update of blastx search against protein sequences in public database.
Homology vs Protein

List of top 10 hits in the results of blastx search against protein sequences in public database.
PSORT

The results of running PSORT(http://psort.ims.u-tokyo.ac.jp/), which is the program to predict the localization of proteins in the cell.
Expression profile

-
VS (DIR, S)

Number of VS-derived clones constituting the contig
VH (FL, L)

Number of VH-derived clones constituting the contig
VF (FL, S)

Number of VF-derived clones constituting the contig
AH (FL, L)

Number of AH-derived clones constituting the contig
AF (FL, S)

Number of AF-derived clones constituting the contig
SL (DIR, L)

Number of SL-derived clones constituting the contig
SS (DIR, S)

Number of SS-derived clones constituting the contig
SH (FL, L)

Number of SH-derived clones constituting the contig
SF (FL, S)

Number of SF-derived clones constituting the contig
CH (FL, L)

Number of CH-derived clones constituting the contig
CF (FL, S)

Number of CF-derived clones constituting the contig
FCL (DIR, L)

Number of FCL-derived clones constituting the contig
FC (DIR, S)

Number of FC-derived clones constituting the contig
FC-IC (SUB)

Number of FC-IC-derived clones constituting the contig