For newcomers and people who want to quickly evaluate whether this package is worth using in the first place, we have a very simple application which allows easy access to OAF's functionality in an easy to use manner. The Bio::Tools::OAZ module provides all the functions. For example, this example will retrieve a OAZ gene from a single sequence file and write it out in GenBank format.
Example of FASTA format:
>my_sequence
TGAACCTCTGCGACTTATCCGCTGAACCTCACTTTGCCGCAGGGAGGCACTGAACAGAGAAACTGCCTTG
TAACAGGTCCCGCCCCTCTCTCTACTCCCTTTCTTATATCAAGAGGGGAAAAACACGGAACTATCTCTAT
CCATTCTGGTCACCATTCGCCTATTACCTCTACTGTTACAAATACCGGATCACCCTCCGGGAGAAGATGC
TGCCTTGTTGTTACAAAAGCATCACTTACAAGGAACAGGAGGACCTGACTCTCCGGCCCCATTGCTGCCT
CCCGTGCTCCTGCCTCCCGTGCTCCTGCCTCCAGTGCTCCTGAGTCCCTAGGAGGCCTCCAGGTGGGTAG
GAGCACTGCACAGGAAAAAGACCACAGCCAGCTTAAAGAACTCTATTCAGCTGGGAACCTGACAGTGCTA
TCAACTGACCCCCTGCTTCACCAAGATCCAGTTCAGTTAGACTTCCACTTTCGTCTTACCCCCCATTCCT
CTGCTCATTGGCACGGCCTTCTGTGTGATCACCGACTCTTCCTGGATATCCCATATCAGGCCTTGGATCA
AGGCAACCGAGAAAGCTTGACAGCAACACTGGAGTATGTGGAGGAGAAAACCAATGTGGACTCTGTGTTT
GTGAACTTCCAAATCGATCGGAAGGACAGAGGTGCCCTGCTGCGAGCCTTTAGCTACATGGGCTTCGAGG
TGGTTAGACCAGATCATCCTGCCCTCCCTCCCTGGGACAATGTCATCTTCATGGTGTATCCCCTTGAAAG
GGACCTTGGCCACCCTGGCCAGTGAGCCTCCCTAAACATGTTCCATCTCTGTGAGGGGTTGGAAACCTCA
ACACACGGGACTCTGAGGCCCAGGATGTGATTTAAGATACTTCCATCCTAGGAAATAAAGGGTAGTGCAA
TC
Your data set should include at least one distinct DNA or RNA sequence and the sequence should be in FASTA format. A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. Lower-case and upper-case letters are both accepted. The full standard IUPAC nucleic acid code is not supported: only A, C, G, T and U symbols are recognized. Numerical digits 0, ..., 9, - and dot . symbols are not accepted.
Example of command-line:
./oaf.pl --format=genbank --sequence=myseq.fasta
Example of result:
gene 207..795
/locus_tag="my_sequence"
/gene="OAZ3"
CDS join(207..320,322..795)
/gene="OAZ3"
/locus_tag="my_sequence"
/note="OAZ3 ORF0: 1.3e-18 ORF1: 9.9e-129"
/inference="FS site: 1"
/ribosomal_slippage
/codon_start=1
/transl_table=1
/product="Ornithine decarboxylase antizyme 3"
/translation="MLPCCYKSITYKEQEDLTLRPHCCLPCSCLPCSCLQCSESLGGL
QVGRSTAQEKDHSQLKELYSAGNLTVLSTDPLLHQDPVQLDFHFRLTPHSSAHWHGLL
CDHRLFLDIPYQALDQGNRESLTATLEYVEEKTNVDSVFVNFQIDRKDRGALLRAFSY
MGFEVVRPDHPALPPWDNVIFMVYPLERDLGHPGQ"
For each sequence, Ornithine decarboxylase Antizyme Finder (OAF) returns a putative Ornithine decarboxylase Antizyme (OAZ). For each sequence, the result is formatted as a
FASTA format, a
GenBank entry fragment, a
raw sequence or an
XML record with a
Document Type Definition (DTD).
If no OAZ is detected, then the message
No Hit is displayed.