Hi Torsten,
I don't have guide or tutorial for Simplifier, but there is
a manuscript (http://www.bioinformation.net/008/97320630008996.pdf).
The parameter -c define the max number of bases ( at 5' and 3') that can be
removed for the software verify if the sequence is redundant. For example:
S1 CGATGCTAAAA
S2 AGATGCTAAAC
The S1 and S2 are different sequences, but if you apply the simplifier over
these sequences using -c 1, the software will try remove one base at the
ends of the sequence and a new sequence S2 will be generated, as bellow:
S1 CGATGCTAAAA
S2 * GATGCTAAA
*
Now, you can see that the sequences are redundant, then Simplifier will
remove the shorter.
Let me know if you have some questions,
Best regards,
Rommel Ramos
Assistant Professor, M.Sc, Ph.D student
Instituto de Ciências Biológicas
Laboratório de Polimorfismo de DNA - Bioinformática
e-mail: rommelramos@ufpa.br http://lattes.cnpq.br/1274395392752454
--
“Pequenas ações que realizamos são melhores que as grandes que planejamos.”
Kung-Fu-Tse
Is there any documentation for 'simplifier' ?
It looks like a useful tool, but all I can find is the jar file, and the 3
parameters, but I don't know how to use -c cut_off.
Is there any documentation for 'simplifier' ?
It looks like a useful tool, but all I can find is the jar file, and the 3 parameters, but I don't know how to use -c cut_off.
Hi Torsten,
I don't have guide or tutorial for Simplifier, but there is
a manuscript (http://www.bioinformation.net/008/97320630008996.pdf).
The parameter -c define the max number of bases ( at 5' and 3') that can be
removed for the software verify if the sequence is redundant. For example:
S1 CGATGCTAAAA
S2 AGATGCTAAAC
The S1 and S2 are different sequences, but if you apply the simplifier over
these sequences using -c 1, the software will try remove one base at the
ends of the sequence and a new sequence S2 will be generated, as bellow:
S1 CGATGCTAAAA
S2 * GATGCTAAA
*
Now, you can see that the sequences are redundant, then Simplifier will
remove the shorter.
Let me know if you have some questions,
Best regards,
Rommel Ramos
Assistant Professor, M.Sc, Ph.D student
Instituto de Ciências Biológicas
Laboratório de Polimorfismo de DNA - Bioinformática
e-mail: rommelramos@ufpa.br
http://lattes.cnpq.br/1274395392752454
--
“Pequenas ações que realizamos são melhores que as grandes que planejamos.”
Kung-Fu-Tse
2012/12/22 Torsten Seemann torst@users.sf.net