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AGenDA - Usage Example
This is an example intended to illustrate how this WWW server works.If you input this pair of sequences, you should be able to reproduce the results presented below.
Input
-
As input, AGenDA requires two sequences in FASTA format.
First sequence:
> M81829ctgcaggcaagcggtcgggtggggagggagggcgcaggcggcgggtgcgcgaggagaaag
ccccagccctggcagccccactggcccccctcagctgggatgttccccaatggcaccgcc
tcctctccttcctcctctcctagccccagcccgggcagctgcggcgaaggcggcggcagc
aggggccccggggccggcgctgcggacggcatggaggagccagggcgaaatgcgtcccag
aacgggaccttgagcgagggccagggcagcgccatcctgatctctttcatctactccgtg
gtgtgcctggtggggctgtgtgggaactctatggtcatctacgtgatcctgcgctatgcc
aagatgaagacggccaccaacatctacatcctaaatctggccattgctgatgagctgctc
atgctcagcgtgcccttcctagtcacctccacgttgttgcgccactggcccttcggtgcg
ctgctctgccgcctcgtgctcagcgtggacgcggtcaacatgttcaccagcatctactgt
ctgactgtgctcagcgtggaccgctacgtggccgtggtgcatcccatcaaggcggcccgc
taccgccggcccaccgtggccaaggtagtaaacctgggcgtgtgggtgctatcgctgctc
gtcatcctgcccatcgtggtcttctctcgcaccgcggccaacagcgacggcacggtggct
tgcaacatgctcatgccagagcccgctcaacgctggctggtgggcttcgtgttgtacaca
tttctcatgggcttcctgctgcccgtgggggctatctgcctgtgctacgtgctcatcatt
gctaagatgcgcatggtggccctcaaggccggctggcagcagcgcaagcgctcggagcgc
aagatcaccttaatggtgatgatggtggtgatggtgtttgtcatctgctggatgcctttc
tacgtggtgcagctggttaacgtgtttgctgagcaggacgacgccacggtgagtcagctg
tcggtcatcctcggctatgccaacagctgcgccaaccccatcctctatggctttctctca
gacaacttcaagcgctctttccaacgcatcctatgcctcagctggatggacaacgccgcg
gaggagccggttgactattacgccaccgcgctcaagagccgtgcctacagtgtggaagac
ttccaacctgagaacctggagtccggcggcgtcttccgtaatggcacctgcacgtcccgg
atcacgacgctctgagcccgggccacgcaggggctctgagcccgggccacgcaggggccc
tgagccaaaagagggggagaatgagaagggaaggccgggtgcgaaagggacggtatccag
ggcgccagggtgctgtcgggataacgtggggctaggacactgacagcctttgatggagga
acccaagaaaggcgcgcgacaatggtagaagtgagagctttgcttataaactgggaaggc
tttcaggctacctttttctgggtctcccactttctgttccttcctccactgcgcttgctc
ctctgaccctccttctattttccccaccctgcaacttctatcctttcttccgcaccgtcc
cgccagtgcagatc
Second sequence:
> M81831tggagccttgagcctagggagggcgcagacagcaagggcgcaaggtgagcgccccagccg
gagccgcaccggcccacttcagctgggatgttccccaatggcaccgcctcctctccctcc
tcttctccaagccccagcccaggcagctgcggggaaggagcctgcagcaggggtccgggg
tccggcgctgcggacggcatggaagagcctggacgaaacgcttcccagaatgggacctta
agcgagggacagggtagcgccattctcatctctttcatctactccgtggtatgcttggtg
ggactgtgtgggaactctatggtcatctatgtgatcctgcgctacgccaagatgaagacc
gctaccaacatctacattctaaacctggctattgctgatgagctgctcatgctcagcgtg
ccctttctggtcacttccacgctgttgcgccactggcccttcggcgcgctactttgccgc
ctggtgctcagcgtggatgcggtcaacatgttcaccagcatctactgtctgactgtgctt
agtgtggaccgctatgtggctgtggtgcacccgatcaaggcagcgcgctaccgtcggccc
actgtggccaaagtagtgaacctgggcgtgtgggtcctgtcattactggttatcttgccc
atcgtggtcttctcacgcaccgcagccaacagcgatggcacggtagcctgcaacatgctc
atgcccgagcccgcccagcgctggttggtgggcttcgtcttatacacatttctcatgggc
ttcctgctgcctgtcggggccatttgcctgtgttatgtgctcatcattgccaagatgcgc
atggtggccctcaaggctggctggcagcagcgcaagcgctcagagcgcaagatcactcta
atggtgatgatggtggtgatggtttttgtcatctgctggatgcctttctacgtggtacag
ctggtcaacgtgttcgccgagcaagacgacgccaccgtgagccagttgtctgtcatcctg
ggctatgccaacagctgtgccaaccccatactctacggcttcctgtcggacaacttcaag
cgctctttccagcgcatcctgtgcctcagctggatggataacgctgcggaggaaccagtc
gactactatgccactgccctgaagagtcgagcctacagcgtggaggacttccagcccgag
aatctggagtctggaggcgttttccgtaatggcacctgcgcttccaggatcagcacgctt
tgagg
Parameters:
- Default parameters
Output
If you run AGenDA with on these two sequences, using the default parameters, you should get an e-mail with the following content:
Dear user of AGenDA,
Your query produced the following results:
The predicted gene model of the sequence J04990 :
|
Gene |
Exon |
Begin |
End |
Score |
Strand |
Frame |
Remainder |
CE_Number |
|
0 |
0 |
100 |
1275 |
1150.519 |
+ |
0 |
0 |
9 |
Protein(s) predicted:
MFPNGTASSPSSSPSPSPGSCGEGGGSRGPGAGAADGMEEPGRNASQNGT
LSEGQGSAILISFIYSVVCLVGLCGNSMVIYVILRYAKMKTATNIYILNL
AIADELLMLSVPFLVTSTLLRHWPFGALLCRLVLSVDAVNMFTSIYCLTV
LSVDRYVAVVHPIKAARYRRPTVAKVVNLGVWVLSLLVILPIVVFSRTAA
NSDGTVACNMLMPEPAQRWLVGFVLYTFLMGFLLPVGAICLCYVLIIAKM
RMVALKAGWQQRKRSERKITLMVMMVVMVFVICWMPFYVVQLVNVFAEQD
DATVSQLSVILGYANSCANPILYGFLSDNFKRSFQRILCLSWMDNAAEEP
VDYYATALKSRAYSVEDFQPENLESGGVFRNGTCTSRITTL*
The predicted gene model of the sequence M96801 :
|
Gene |
Exon |
Begin |
End |
Score |
Strand |
Frame |
Remainder |
CE_Number |
|
0 |
0 |
88 |
1263 |
1143.396 |
+ |
0 |
0 |
9 |
Protein(s) predicted:
MFPNGTASSPSSSPSPSPGSCGEGACSRGPGSGAADGMEEPGRNASQNGT
LSEGQGSAILISFIYSVVCLVGLCGNSMVIYVILRYAKMKTATNIYILNL
AIADELLMLSVPFLVTSTLLRHWPFGALLCRLVLSVDAVNMFTSIYCLTV
LSVDRYVAVVHPIKAARYRRPTVAKVVNLGVWVLSLLVILPIVVFSRTAA
NSDGTVACNMLMPEPAQRWLVGFVLYTFLMGFLLPVGAICLCYVLIIAKM
RMVALKAGWQQRKRSERKITLMVMMVVMVFVICWMPFYVVQLVNVFAEQD
DATVSQLSVILGYANSCANPILYGFLSDNFKRSFQRILCLSWMDNAAEEP
VDYYATALKSRAYSVEDFQPENLESGGVFRNGTCASRISTL*
Explanation:
Gene: gene number (for reference)
Exon: exon number (for reference)
Strand: DNA strand (+ = input strand; - = opposite strand)
Begin: beginning of exon
End: end point of exon
Score: Total score
Frame: reading frame (0, 1, 2)
Remainder: Remainder (length of the exon modulo 3)
CE_Number: Reference number for the exon in the Candidate Exons tables
You can visit this link to look at the visualisation of results:
result.html
For looking at the candidates exons detected by the AGenDA software visit
cer1.html
and
cer2.html
for the first and the second sequence respectively.
Optional user comments: "this is just an example"
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