Commit 78fed1da by Diego Rubert

Merge branch 'master' of git.facom.ufms.br:diego/ffdcj-sim

parents 93057103 5959230e
Showing with 15 additions and 12 deletions
......@@ -68,7 +68,7 @@ Example:
2 1 -1 0.3
3 2 1 0.4
```
1 means a direct correspondence and -1 a reverse correspondence. Notice, however, that this file format does not define explicitly the total order of genes in genomes, this is done by an algorithm embedded in the code (courtesy of Daniel Doerr) that constructs *a* compatible total order. As an example, for the input:
Relative orientation 1 means a direct correspondence and -1 a reverse correspondence. Notice, however, that this file format does not define explicitly the total order of genes in genomes, this is done by an algorithm embedded in the code (courtesy of Daniel Doerr) that constructs *a* compatible total order. As an example, for the input:
```
1 1 1 0.64753765
2 1 -1 0.76287652
......@@ -141,9 +141,9 @@ Example for Homo Sapiens:
1. Look for homo sapiens in genome database at NCBI (e.g. https://www.ncbi.nlm.nih.gov/genome/?term=homo+sapiens)
2. For X chromosome row click at "RefSeq" column (ex. NC_000023.11)
2. In the X chromosome row, click at "RefSeq" column (ex. NC_000023.11)
3. Download GB file by clicking at "Send to" with "Complete Record", "File" (in "Choose Destination) and "GenBank (full)" (at "Format") selected
3. Download GB file by clicking at "Send to" with "Complete Record", "File" (in "Choose Destination") and "GenBank (full)" (at "Format") options selected
After downloading GBs for all species:
......
......@@ -61,8 +61,10 @@ All options are relative to heuristics, not to the ILP.
-----------
File format
-----------
The file format is very simple and defines two **UNICHROMOSOMAL** genomes (although
could be easily extended to multiple chromosomes). Each line is composed by 4 fields:
The file format is very simple and defines two **UNICHROMOSOMAL** genomes
(although could be easily extended to multiple chromosomes). Each line is
composed by 4 fields:
1. Gene number in genome A
2. Gene number in genome B
......@@ -75,11 +77,11 @@ Example:
2 1 -1 0.3
3 2 1 0.4
1 means a direct correspondence and -1 a reverse correspondence.
Notice, however, that this file format does not define explicitly
the total order of genes in genomes, this is done by an algorithm
embedded in the code (courtesy of Daniel Doerr) that constructs
*a* compatible total order. As an example, for the input:
Relative orientation 1 means a direct correspondence and -1 a reverse
correspondence. Notice, however, that this file format does not define
explicitly the total order of genes in genomes, this is done by an algorithm
embedded in the code (courtesy of Daniel Doerr) that constructs *a* compatible
total order. As an example, for the input:
1 1 1 0.64753765
2 1 -1 0.76287652
......@@ -173,10 +175,11 @@ Example for Homo Sapiens:
1. Look for homo sapiens in genome database at NCBI
(https://www.ncbi.nlm.nih.gov/genome/?term=homo+sapiens)
2. For X chromosome row click at "RefSeq" column (ex. NC_000023.11)
2. In the X chromosome row, click at "RefSeq" column (ex. NC_000023.11)
3. Download GB file by clicking at "Send to" with "Complete Record", "File"
(in "Choose Destination) and "GenBank (full)" (at "Format") selected
(in "Choose Destination") and "GenBank (full)" (at "Format") options
selected
After downloading GBs for all species:
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or sign in to comment