RSAT - Neighbour ORFs manual
Name
Description
Options
Query: each line is considered as a separate query.
The query list can take three alternative formats:
- ORF identifier:
the first word of each line contains an ORF identifier (e.g.: YFL021W).
- Chromosomal positions:
- The first word of each line is the chromosome number (in latin or arab notation).
- The second word is the start position
- The 3d word is the end position (optional)
- The 4th word is an identifier (optional)
Examples of chromosomal positions
IX 20000 (a single position in the chromosome IX)
XIII 20000 40000 (a pair of coordinates specifying a segment of chromosome XIII
- Genome search result: the output of a whole genome search
Output format
Each line of the output correspond to one line fro the query.
upstream-downstream
- Q_id query identifier
- Q_gene query gene name
- Q_chr query chromosome
- Q_start query start position
- Q_end query end position
- U_ORF upstream neighbour ORF identifier
- U_gene upetrsam neighbour gene name
- U_dist distance between query position and upstream neighbour
- D_ORF downstream neighbour ORF identifier
- D_gene downstream neighbour gene name
- D_dist distance between query position and downstream neighbour
left-right
- Q_id query identifier
- Q_gene query gene name
- Q_chr query chromosome
- Q_start query start position
- Q_end query end position
- L_ORF left neighbour ORF identifier
- L_gene left neighbour gene name
- L_dist distance between query position and left neighbour
- R_ORF right neighbour ORF identifier
- R_gene right neighbour gene name
- R_dist distance between query position and right neighbour
Link to database
When this option is active, ORF identifier
are automatically linked to the correspondent entry in a yeast genome
database (Standford or
MIPS).