'- >./cyntenator -'
'- program -t guide-tree -h homology_type ... -'
'- guide-tree: -'
'- -t "((rat.txt mouse.txt ) human.txt)" -'
'- Homology: -'
'- -h id -'
'- -h blast [file] -'
'- -h orthologs [file] -'
'- -h phylo [file] [weighted_tree] -'
'- -'
'- Alignment Parameters: -'
'- -thr threshold (4) -'
'- -gap gap (-2) -'
'- -mis mismatch (-3) -'
'- -'
'- Filter options: -'
'- -filter [int] best alignments or only unique assignments n=0 (100) -'
'- -coverage [int] each gene may occur only c times in alignments (2) -'
'- -length [int] minimum alignment length treshold (1) -'
'- -last prints only the alignments at the last step -'
'- -'
'- Output: -'
'- -o output file -'

'- #alignment CFX.txt HSX.txt MMX.txt -'
'- Alignment 1 9.18021 -'
'- 0.348995 ENSCAFG00000016080 (+) ENSG00000184205 (+) ENSMUSG00000041096 (+) -'
'- 1.89445 ENSCAFG00000016133 (-) ENSG00000126012 (-) ENSMUSG00000025332 (-) -'
'- 0.348995 - (.) ENSG00000204349 (+) - (.) -'
'- 1.36421 ENSCAFG00000016179 (-) ENSG00000124313 (-) ENSMUSG00000041115 (-) -'
'- 2.88981 ENSCAFG00000016241 (-) ENSG00000072501 (-) ENSMUSG00000041133 (-) -'
'- 3.3294 ENSCAFG00000016274 (+) ENSG00000158423 (+) ENSMUSG00000025257 (+) -'
'- 3.77215 ENSCAFG00000016277 (-) ENSG00000072506 (-) ENSMUSG00000025260 (-) -'
'- 5.3176 ENSCAFG00000016311 (-) ENSG00000086758 (-) ENSMUSG00000025261 (-) -'
'- 6.71358 ENSCAFG00000016389 (-) ENSG00000172943 (-) ENSMUSG00000041229 (-) -'
'- 5.16812 - (.) - (.) ENSMUSG00000067230 (+) -'
'- 6.57727 ENSCAFG00000016414 (-) ENSG00000184083 (-) ENSMUSG00000025262 (-) -'
'- 5.03181 - (.) - (.) ENSMUSG00000072901 (+) -'
'- 6.57727 ENSCAFG00000016427 (-) ENSG00000196632 (-) ENSMUSG00000041245 (-) -'
'- 6.86235 ENSCAFG00000016440 (+) ENSG00000158526 (+) ENSMUSG00000025264 (+) -'
'- 8.19742 ENSCAFG00000016444 (-) ENSG00000102302 (-) ENSMUSG00000025265 (-) -'
'- 9.18021 ENSCAFG00000016455 (+) ENSG00000130119 (+) ENSMUSG00000025266 (+) -'

'- ./cyntenator -t "(HSX.txt MMX.txt)" -h phylo HSCFMM.blast -'
'- "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5)" > human_mouse-'

'- ./cyntenator -t "(human_mouse CFX.txt)" -h phylo HSCFMM.blast -'
'- "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5)" > test1.txt-'

'- ./cyntenator -last -t "((HSX.txt MMX.txt) CFX.txt)" -h phylo HSCFMM.blast -'
'- "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5)" > test2.txt-'

this will create a binary executable named cyntenator. The Makefile uses the g++ compiler,\\

Obligatory arguments are the guiding tree which specifies the order in which genomes are\\
aligned. It can be specified by a notation in parantheses (e.g. "((rat.txt mouse.txt ) \\
human.txt)"). In this example rat.txt, mouse.txt, and human.txt are the gene annotation \\

The second argument which is needed is the type of homology and a corresponding \\
similarity file. The type id assigns a match, whenever two IDs (GENE Symbols,
transcription [[<<]] factor binding sites or any other Marker) are equal.
The "orthology" type assigns matches [[<<]] for pair of genes that are given in a correspondance file, furthermore
correspondances can [[<<]]
be assigned simililarity scores like BLAST bitscores, this is the [[<<]]
option, that we used in the Syntenator approach. In order to weight matches by sequence
[[<<]]

tree [[<<]] has to be defined with weights specified by [:WEIGHT] after each closing bracket [[<<]]

note can [[<<]] be omitted.

There are three possible input formats which can be used as annotation files. The format [[<<]]

'''genome''' is the standard format for alignment of genomes. Annotations can be obtained [[<<]]
from the [[http://www.ensembl.org | EnsEMBL]] database and should contain whitespace[[<<]]
separated gene coordinates (ID,CHROMOSOME,START,END,STRAND, see HSX.txt as example). [[<<]]
The same is true for the '''sequence''' format which should be used for alignment using[[<<]]
IDs as similarity measure. The only difference is that the genome format requires unique[[<<]]
IDs and merges redundant gene annotations which come from different transcripts.[[<<]]

The '''alignment''' format is the output format of cyntenator. In the header the original[[<<]]
annotation files are enlisted. The following lines show all computed alignments, sorted [[<<]]
by score and uniqueness. An Alignment starts with the word Alignment followed by a number
[[<<]] and then a score. Each following line starts with a score for this row and the [[<<]] aligned genes with their

It is possible to compute pairwise alignments parallel and then compute the multiple [[<<]]

[[<<]]

'- ./cyntenator -t "(HSX.txt MMX.txt)" -h phylo HSCFMM.blast "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5)" > human_mouse-'

'- ./cyntenator -t "(human_mouse CFX.txt)" -h phylo HSCFMM.blast "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5)" > test1.txt-'

'- ./cyntenator -last -t "((HSX.txt MMX.txt) CFX.txt)" -h phylo HSCFMM.blast "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5)" > test2.txt-'

test1.txt and test2.txt will contain the same alignments in the end. Not, that the -last
[[<<]]

[[<<]]

[[<<]]

this will create a binary executable named cyntenator. The Makefile uses the g++ compiler,
in general it should be possible to compile the program on windows but this was not
tested.

Obligatory arguments are the guiding tree which specifies the order in which genomes are
aligned. It can be specified by a notation in parantheses (e.g. "((rat.txt mouse.txt )
human.txt)"). In this example rat.txt, mouse.txt, and human.txt are the gene annotation
files for the respective species.


The second argument which is needed is the type of homology and a corresponding
similarity file. The type "id" assigns a match, whenever two IDs (GENE Symbols,
Transcription factor Binding sites or any other Marker) are equal. The "orthology" type
assigns matches for pair of genes that are given in a correspondance file, furthermore
correspondances can be assigned simililarity scores like BLAST bitscores, this is the
option, that we used in the Syntenator approach. In order to weight matches by sequence
similarity and phylogenetic distance, in addition to the BLAST file, a weighted species
tree has to be defined with weights specified by [:WEIGHT] after each closing bracket
(e.g. "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5):1" ). The final weight at the root
note can be omitted.

There are three possible input formats which can be used as annotation files. The format
has to be specified in the first row of the file:

'''genome''' is the standard format for alignment of genomes. Annotations can be obtained
from the [[http://www.ensembl.org | EnsEMBL]] database and should contain whitespace
separated gene coordinates (ID,CHROMOSOME,START,END,STRAND, see HSX.txt as example).
The same is true for the '''sequence''' format which should be used for alignment using
IDs as similarity measure. The only difference is that the genome format requires unique
IDs and merges redundant gene annotations which come from different transcripts.

The '''alignment''' format is the output format of cyntenator. In the header the original annotation files are enlisted. The following lines show all computed alignments, sorted
by score and uniqueness.
An Alignment starts with the word Alignment followed by a number and then a score. Each
following line starts with a score for this row and the aligned genes with their
orientation. "-" characters denote gaps.

It is possible to compute pairwise alignments parallel and then compute the multiple
genome alignments by specyfing the alignment output files as input. The following 2 runs
are test runs to see, whether cyntenator can read pairwise alignments

test1.txt and test2.txt will contain the same alignments in the end. Not, that the -last
option is used in the second example in order to report only the alignments created from
the HSX-MMX vs CFX multiple species comparison.

This software was written by Christian Rödelsperger and is distributed under GNU General
Public License (GPL)

!! Documentation


!!! Installation

In order to install cyntenator on linux, simply type

>make

this will create a binary executable named cyntenator. The Makefile uses the g++ compiler,
in general it should be possible to compile the program on windows but this was not tested.



!!! Usage

If cyntenator is called without any arguments, a help message is printed on standard output


>./cyntenator
program -t guide-tree -h homology_type ...
guide-tree:
-t "((rat.txt mouse.txt ) human.txt)"
Homology:
-h id
-h blast [file]
-h orthologs [file]
-h phylo [file] [weighted_tree]

Alignment Parameters:
-thr threshold (4)
-gap gap (-2)
-mis mismatch (-3)

Filter options:
-filter [int] best alignments or only unique assignments n=0 (100)
-coverage [int] each gene may occur only c times in alignments (2)
-length [int] minimum alignment length treshold (1)
-last prints only the alignments at the last step

Output:
-o output file



Obligatory arguments are the guiding tree which specifies the order in which genomes are aligned. It can be specified by a notation in parantheses (e.g. "((rat.txt mouse.txt ) human.txt)"). In this example rat.txt, mouse.txt, and human.txt are the gene annotation files for the respective species.

The second argument which is needed is the type of homology and a corresponding similarity file. The type "id" assigns a match, whenever two IDs (GENE Symbols, Transcription factor Binding sites or any other Marker) are equal. The "orthology" type assigns matches for pair of genes that are given in a correspondance file, furthermore correspondances can be assigned simililarity scores like BLAST bitscores, this is the option, that we used in the Syntenator approach. In order to weight matches by sequence similarity and phylogenetic distance, in addition to the BLAST file, a weighted species tree has to be defined with weights specified by [:WEIGHT] after each closing bracket (e.g. "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5):1" ). The final weight at the root note can be omitted.

Alignment paramters can be modified via the options thr gap and mis.


!!! File Formats

There are three possible input formats which can be used as annotation files. The format has to be specified in the first row of the file:

#genome
#sequence
#alignment

'''genome''' is the standard format for alignment of genomes. Annotations can be obtained from the [[http://www.ensembl.org | EnsEMBL]] database and should contain whitespace separated gene coordinates (ID,CHROMOSOME,START,END,STRAND, see HSX.txt as example).
The same is true for the '''sequence''' format which should be used for alignment using IDs as similarity measure. The only difference is that the genome format requires unique IDs and merges redundant gene annotations which come from different transcripts.

The '''alignment''' format is the output format of cyntenator. In the header the original annotation files are enlisted. The following lines show all computed alignments, sorted by score and uniqueness.
An Alignment starts with the word Alignment followed by a number and then a score. Each following line starts with a score for this row and the aligned genes with their orientation. "-" characters denote gaps.


#alignment CFX.txt HSX.txt MMX.txt
Alignment 1 9.18021
0.348995 ENSCAFG00000016080 (+) ENSG00000184205 (+) ENSMUSG00000041096 (+)
1.89445 ENSCAFG00000016133 (-) ENSG00000126012 (-) ENSMUSG00000025332 (-)
0.348995 - (.) ENSG00000204349 (+) - (.)
1.36421 ENSCAFG00000016179 (-) ENSG00000124313 (-) ENSMUSG00000041115 (-)
2.88981 ENSCAFG00000016241 (-) ENSG00000072501 (-) ENSMUSG00000041133 (-)
3.3294 ENSCAFG00000016274 (+) ENSG00000158423 (+) ENSMUSG00000025257 (+)
3.77215 ENSCAFG00000016277 (-) ENSG00000072506 (-) ENSMUSG00000025260 (-)
5.3176 ENSCAFG00000016311 (-) ENSG00000086758 (-) ENSMUSG00000025261 (-)
6.71358 ENSCAFG00000016389 (-) ENSG00000172943 (-) ENSMUSG00000041229 (-)
5.16812 - (.) - (.) ENSMUSG00000067230 (+)
6.57727 ENSCAFG00000016414 (-) ENSG00000184083 (-) ENSMUSG00000025262 (-)
5.03181 - (.) - (.) ENSMUSG00000072901 (+)
6.57727 ENSCAFG00000016427 (-) ENSG00000196632 (-) ENSMUSG00000041245 (-)
6.86235 ENSCAFG00000016440 (+) ENSG00000158526 (+) ENSMUSG00000025264 (+)
8.19742 ENSCAFG00000016444 (-) ENSG00000102302 (-) ENSMUSG00000025265 (-)
9.18021 ENSCAFG00000016455 (+) ENSG00000130119 (+) ENSMUSG00000025266 (+)


It is possible to compute pairwise alignments parallel and then compute the multiple genome alignments by specyfing the alignment output files as input. The following 2 runs are test runs to see, whether cyntenator can read pairwise alignments

PART 1: compute pairwise, read pairwise, compute tripple

./cyntenator -t "(HSX.txt MMX.txt)" -h phylo HSCFMM.blast "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5):1" > human_mouse
./cyntenator -t "(human_mouse CFX.txt)" -h phylo HSCFMM.blast "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5):1" > test1.txt


PART 2: compute pairwise, compute tripple

./cyntenator -last -t "((HSX.txt MMX.txt) CFX.txt)" -h phylo HSCFMM.blast "((HSX.txt:1.2 MMX.txt:1.3):0.5 CFX.txt:2.5):1" > test2.txt

test1.txt and test2.txt will contain the same alignments in the end. Not, that the -last option is used in the second example in order to report only the alignments created from the HSX-MMX vs CFX multiple species comparison.

!!! License

This software was written by Christian Rödelsperger and is distributed under GNU General Public License (GPL)