DESCRIPTION: Tool for trimming EST (DNA) sequences
##
## SYNTAX: est_trimmer.pl <FASTAfile> [-amb=n,win] [-tr5=(A|C|G|T),n,win]
## [-tr3=(A|C|G|T),n,win] [-cut=min,max] [-id=name]
## [-help]
##
## <FASTAfile> Single file in FASTA format containing the sequence(s).
## [-amb=n,win] Removes distal stretches containing "n" ambiguous bases in
a
## "win" bp sized window.
## [-tr5=N,n,win] Removes stretches of the given type N={A,C,G,T} from the 5
‘
## end. Value "n" defines the min. accepted repeat number of
"N"
## in a 5‘ window of the size "win".
## [-tr3=N,n,win] according to [-tr5] for the 3‘ end.
## [-cut=min,max] Sets min. value for cutoff and max. sequence size.
## [-id=name] Optional. Final results are stored in "name".results, wher
eas
## processing steps are listed in "name".log. If not used,
## extensions are appended to <FASTAfile>.
## [-help] Further descriptions. Use "EST_trimmer.pl -help".
##
## Arguments can be used plurally and are processed according to their order
.
##
## EXAMPLE: est_trimmer.pl ESTs -amb=2,50 -tr5=T,5,50 -tr3=A,5,50 -cut=100,700
## ____________________________________________________________________________
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##
repeatmasker 是个比较复杂的软件，参数比较多，此外还必须在本机装过crossmatch或者wu-blast要多看手册根据自己实际情况设定。其软件有个数据库，每年都更新，本地计算的必须要注意。
