SILMUT

Program Description, Input Files And Output Results

Prelude

The Web front-end of SILMUT and TABLE programs are developed in Java by Susan Yu in Center for Genomic Sciences at West Penn Allegheny Health System.

The original Dos version of SILMUT and TABLE are from

Raj Shankarappa, Ph.D. Department: Infcts Diseases/Microbiology, PUBHL A449 ,BSTWR 1540 Pittsburgh, PA 15213 and
K Vijayananda, Department of Computer Science, University of Maryland, College Park, MD 20740

Silmut program identifies the silent mutation potential for the introduction of 6-base restriction enzyme sequences by translating the RE recognition sequence in three reading frames to obtain a set of amino acid motifs and finding a match for the amino acid motif with the amino acid sequence provided as the input. Thirty selected restriction enzymes which do not contain degeneracy in their recognition sites have been provided in file dbase2. This file can be edited in a DOS text editor to remove any restriction enzyme sequences from being recognized or add new 6-base sequences.

The maximum number of restriction enzyme sites that can be included in this file is 100.

Table program provides the sets of amino acid motifs obtained by translation of any 6-base sequence in three reading frames.

Table program provides a table/listing of amino acid motifs obtained by translating a 6-base sequence in three reading frames. Translation in the first reading frame yields a sequence of two amino acids, while translation in second and third reading frames will yield degeneracies in the first and third position. Each of these amino acid motifs is separated in the output for clarity. Due to longer lines, the end of the line might be wrapped onto the next line. You may correct for this by editing and printing the file using a word processing program after setting a wider margins or setting smaller sized letters.

The work is based on the following publications.

1. B. Shankarappa, D.A. Sirko, and G.D. Ehrlich. A General Method for the Identification of Regions Suitable for Site-Directed Silent Mutagenesis. BioTechniques 12, No. (3): 382-384

2. B. Shankarappa, K. Vijayananda, and G.D. Ehrlich. SILMUT: A Computer program for the Identification of Regions Suitable for Silent Mutagenesis to Introduce Restriction Enzyme Recognition Sequences. BioTechniques 12, No. (6):

Input sequence file for SILMUT

The input file must be in a DOS text format and has only three lines in the file.

Line 1. The file should contain 1 (for AA) or 2 (for NA) in the first line,

Line 2. The sequence of nucleic/amino acid in the second line without line break

Line 3. and the number 3 (for exiting) in the third line

We recommend that you use a DOS editor. Also make sure you save the file in a DOS format.

Default Input files: dbase1 and dbase2

The default inputs are the files dbase1 and dbase2, for translation of recognition sequences of 30 commonly used restriction enzymes. If you want to change the codon specificities, you have to edit the file dbase1. If you want to add or delete any restriction enzyme sites, or any other 6-base sites like splice sites etc., you need to edit the file dbase2. This editing can be done in a DOS environment using any of the softwares like Q.exe. If you use other softwares like WordPerfect, make sure the file is saved as a DOS text file. Also, make sure that the spacing and other format of the files dbase1 and dbase2 are retained as before.

Run the program in command line

From MS dos:

Unzip the downloaded file to a folder. Launch MS dos consol and then change to the folder where program unzipped
Type silmut.exe -i <input file> [-o <output file>] or type table.exe without any parameter

From Unix/Linux 32-bit:

Unzip the downloaded file to a folder. Launch command consol or terminal and then change to the unzipped folder
Give permission to run for silmutLx and tableLx by issuing chmod +x tableLx, and chmod +x silmutLx.
If the input file is prepared in Windows operating system, convert it to the unix format using command dos2unix <input file>
Type silmutLx -i <input file> -o <output file> -d1 <dbase1 file> -d2 <dbase2 file> or
Type tableLx -d1 <dbase1 file> -d2 <dbase2 file>
If the program does not recoginize the input file, always run dos2unix to convert to unix format

Sample Output:

SILMUT:

-----------------------------------------------------------------------

GPGR

ApaI Cfr9I/SmaI/XmaI

Cfr9I/SmaI/XmaI

EagI/XmaIII

Position in the input string: 1

Amino acid string at this position: GP

Restriction Enzyme site/s that can be introduced at this position: ApaI

Position in the input string: 1

Amino acid string at this position: GPG

Restriction Enzyme site/s that can be introduced at this position: Cfr9I/SmaI/XmaI

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TABLE

Following is the output from TABLE program for 30 selected RE sites. Please adujust the margins so that all the data is in one line. The order of the contents of the following table is RE, Recognition site, 1st and 2nd AA obtained in the first reading frame, 1,2,3rd AA obtained from 2nd reading frame, and 1,2,3rd AA obtained from the third reading frame.

HindIII AAGCTT K L XQKE A FLSYXCW LSXPQRITKVAEG S FL

MluI ACGCGT T R YHND A FLSYXCW LSXPQRITKVAEG R V

SpeI ACTAGT T S YHND X FLSYXCW LSXPQRITKVAEG L V

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