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rmes.gfam
Generation of a Family File


Description Usage Options Output file Examples


Description

Families of words can be analyzed by using the program rmes.gaussien.
The families of interest are then described into a family file according to a specific format. For convenience, the command rmes.gfam can automically generate particular family files. These families are degenerated words or hairpin motifs on the {a,g,c,t,n} alphabet (n means any of the four bases) and should be represented by a generic pattern using the a,g,c,t,n,# and '.' characters (as described below).

Usage

rmes.gfam -p[attern] <pattern> 
          [-english] 
          [-t[itle] <title>] 
	  > family-file

Options

-p[attern] <pattern>
<pattern> represents the generic name of the families that have to be generated. It is a string of characters among #,a,g,c,t,n and the character '.'.
If a,g,c,t
The character is left unchanged in all family names and in all words.
If n
Words within a family are generated by replacing the n in the family name successively by a,g,c,t. (Example 1)
If #
This # allow to generate the name of the families since it is replaced successively by a,g,c,t. (Example 2)
If '.'
Characters points can only be at the right-end of the pattern. Words within a family are generated by replacing the point in the family name by the complementary letter of the letter that is at the symmetric position at the beginning of the current word. It allows to generate pseudo-palindromic words or hairpin motifs. (Example 3)
-english or -eng
When set, the messages are in english.
By default, they are in french.
-t[itle] <title>
When this option is set, <title> contains the string to put as title in the family-file.
By default, it is an empty string.

Sommaire

Examples

1- We generate a unique family of 4-words: the degenerated word gntggtgg. The n is successively replaced by a,g,c,t in this family to generate each word. 
rmes.gfam -p gntggtgg -t "CHI motif of H. Influenzae" -english > fam_CHI-Hinf

The family-file is called fam_CHI-Hinf and contains: 

CHI motif of H. Influenzae #    <---- a title
1				<---- number of families
4				<---- number of words in the family
8				<---- length of words
 gntggtgg
     gatggtgg
     ggtggtgg
     gctggtgg
     gttggtgg

Sommaire

2- We generate 16384 families. Each name of family contains the letter n in position 2, and the character # is replaced successively replaced by a,g,c,t by beginning at the end of the name of the family. So, the first name of the family is anaaaaaa and the last one is tntttttt. Inside each family, the letter n is successively replaced by a,g,c,t to generate 4 words of length 8. 

rmes.gfam -p #n###### -t "family xnxxxxxx" -english > fam.xnxxxxxx

The family-file is called fam.xnxxxxxx and contains: 

family xnxxxxxx #	<---- a title
16384			<---- number of families
4			<---- number of words in the families
8			<---- length of words
 anaaaaaa
     aaaaaaaa
     agaaaaaa
     acaaaaaa
     ataaaaaa
 anaaaaag
     aaaaaaag
     agaaaaag
     acaaaaag
     ataaaaag

...

 tntttttc
     tatttttc
     tgtttttc
     tctttttc
     tttttttc
 tntttttt
     tatttttt
     tgtttttt
     tctttttt
     tttttttt

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3- We generate a unique family of 64 words. The 9-words generated form a hairpin motif starting by acg and ending by the complementary of acg namely cgt. The 3 letters n are successively replaced by a,g,c,t. 

rmes.gfam -p acgnnn... -t "family acgnnn..." -english > fam_acgnnn..._out

The family-file is called fam_acgnnn..._out and contains: 

family acgnnn... #	<---- a title
1			<---- number of families
64			<---- number of words in the families
9			<---- length of words
 acgnnncgt
     acgaaacgt
     acgaagcgt
     acgaaccgt

...

     acgttgcgt
     acgttccgt
     acgtttcgt

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4- We generate a set of 64 families of hairpin motifs with a loop of size 3. The families are named aaannnttt, aagnnnctt, and so on. Because of the three unspecified bases, each family contains 64 words or hairpin motifs. 

rmes.gfam -p ###nnn... -t "family xxxnnn..." -english > fam_xxxnnn..._out

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