fasta-get-markov

[CharlesEGrant]

Originally posted by skdhanraj 20 Sep 2006

i am not able to make background frequency file (-bfile) using fasta-get-markov 
of the order 5. 
i need to know the syntax for using this program as where i have to specify my sequence file (in fasta format). 
thx in advance 
surendra

[CharlesEGrant]

Originally posted by Bendan 21 Sep 2006

skdhanraj wrote:

i am not able to make background frequency file (-bfile) using fasta-get-markov  of the order 5.  i need to know the syntax for using this program as where i have to specify my sequence file (in fasta format).  thx in advance  surendra

Code:

#fasta-get-markov -help    USAGE:          fasta-get-markov [-m <order>] [-p]          [-m <order>]    order of Markov model to use; default 0          [-p]            use protein alphabet; default: use DNA alphabet          Estimate a Markov model from a FASTA file of sequences.          Ignores (removes) ambiguous characters before computing          the model.          Reads standard input.          Writes standard output.

[CharlesEGrant]

Originally posted by skdhanraj 26 Sep 2006

yeah i am getting the usage of this program ..........what i mean to ask is- the syntax of this program i.e. 

#./fasta-get-markov -m 5 seq1.fasta 

its not working , it simply prints the usage what u have writtin. is there any other program which can generate backgroud markov model for the order 5???

[CharlesEGrant]

Originally posted by Bendan 28 Sep 2006

skdhanraj wrote:

yeah i am getting the usage of this program ..........what i mean to ask is- the syntax of this program i.e.  #./fasta-get-markov -m 5 seq1.fasta  its not working , it simply prints the usage what u have writtin. is there any other program which can generate backgroud markov model for the order 5???

It's a bit obscure from the usage guide, but the way to read standard input is to use "<", and to write standard ouput is to use ">". 

So

Code:

fasta-get-markov -m 5 < seq1.fasta > my_fifth_order_profile