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Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 09:26:29 -0000

--- v11
+++ v12
@@ -30,8 +30,14 @@
 •  For FDR corrected identification files from analmod program, results are tabulated to ID_SITES and ID_PSMS which help in in-depth analysis and data provenance for sites and modified peptides of interest.

 ##Quick start guide
+
+##Input/output
+
 ##Limitations
-##Input/output
+
+As all good things have some bad qualities so do ModST has.
+1. ModST can be run for only mgf files. since the package is written for mgf files only. though in future it will be extended for other formats read by MODa.
+2. On machines with only 1 core it can give only automation and no parallezation. but in this age of technology boom, 1 core systems hardly exist.

 ##**Help**
 For any help, please email amit.yadav@thsti.res.in, suruchi@thsti.res.in or post in our [support](https://sourceforge.net/projects/modst/support) forum.

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 09:22:09 -0000

--- v10
+++ v11
@@ -19,6 +19,16 @@
 Docmentation can be found [here](https://sourceforge.net/p/modst/wiki/documentation/) or with the downloaded software.

 ##Advantages
+There are several advantages of ModST apart from the speed and configurable features:
+•  It is platform independent (since both Perl & Java are platform independent) and can run on any operating system.
+•  It integrates MODa results for ease of analysis for individual sites of modifications and statistical analysis from          complete set of results.
+•  It compiles protein level information, which helps in analyzing the fraction of modified peptides for every protein in the sample.
+•  Using the corrected PTM masses, users can annotate modifications unambiguously using any PTM database like RESID, DeltaMass or Unimod with better accuracy.
+•  With better PTM annotation, the localization errors can also be corrected as the known PTMs have specific amino acid sites of occurrence.
+•  Using the newly corrected PTM table frequencies, users can make better biological interpretations of the masses present.  
+•  This pipeline also provides tabulated results for MODa output file which can be used to find the peptide or modification of interest in complete set of results. 
+•  For FDR corrected identification files from analmod program, results are tabulated to ID_SITES and ID_PSMS which help in in-depth analysis and data provenance for sites and modified peptides of interest. 
+
 ##Quick start guide
 ##Limitations
 ##Input/output

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 09:20:18 -0000

--- v9
+++ v10
@@ -4,7 +4,7 @@
 ModST can be downloaded from [here](https://sourceforge.net/projects/modst/files/?source=navbar). Please find the latest version and download from the above link.

 ##**Background**
-[Post-translational Modifications](https://en.wikipedia.org/wiki/Post-translational_modification) (PTMs) are the covalent or enzymatic modifications attached to the proteins co or post-translationally.
+[Post-translational Modifications](https://en.wikipedia.org/wiki/Post-translational_modification) (PTMs) are the covalent or enzymatic modifications attached to the proteins co or post-translationally. they are required to regulate biological functions of a protein. for information on some widely studied modifications read [here](https://www.thermofisher.com/in/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-post-translational-modification.html).

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 09:18:46 -0000

--- v8
+++ v9
@@ -4,6 +4,7 @@
 ModST can be downloaded from [here](https://sourceforge.net/projects/modst/files/?source=navbar). Please find the latest version and download from the above link.

 ##**Background**
+[Post-translational Modifications](https://en.wikipedia.org/wiki/Post-translational_modification) (PTMs) are the covalent or enzymatic modifications attached to the proteins co or post-translationally.

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 09:15:11 -0000

--- v7
+++ v8
@@ -3,16 +3,27 @@

 ModST can be downloaded from [here](https://sourceforge.net/projects/modst/files/?source=navbar). Please find the latest version and download from the above link.

+##**Background**
+
+
+
 ##**Installation**
 Detailed instructions are provided with downloaded documentation for version specific installation. This will require-
-1. * [Perl](http://www.activestate.com/activeperl)
-* [MODa](http://prix.hanyang.ac.kr/download/moda.jsp)
-* [Java](https://www.java.com/en/download/)
-* [Parallel::ForkManager](http://search.cpan.org/~dlux/Parallel-ForkManager-0.7.5/ForkManager.pm) from cpan
+1. [Perl](http://www.activestate.com/activeperl)
+2. [MODa](http://prix.hanyang.ac.kr/download/moda.jsp)
+3. [Java](https://www.java.com/en/download/)
+4. [Parallel::ForkManager](http://search.cpan.org/~dlux/Parallel-ForkManager-0.7.5/ForkManager.pm) from cpan

 ##**Documentation**
 Docmentation can be found [here](https://sourceforge.net/p/modst/wiki/documentation/) or with the downloaded software.

+##Advantages
+##Quick start guide
+##Limitations
+##Input/output
+
 ##**Help**
 For any help, please email amit.yadav@thsti.res.in, suruchi@thsti.res.in or post in our [support](https://sourceforge.net/projects/modst/support) forum.
+
+##**Bug reports**
 For Bug reports, use the [ticket](https://sourceforge.net/p/modst/tickets/) system.

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 08:57:50 -0000

--- v6
+++ v7
@@ -5,7 +5,7 @@

 ##**Installation**
 Detailed instructions are provided with downloaded documentation for version specific installation. This will require-
-* [Perl](http://www.activestate.com/activeperl)
+1. * [Perl](http://www.activestate.com/activeperl)
 * [MODa](http://prix.hanyang.ac.kr/download/moda.jsp)
 * [Java](https://www.java.com/en/download/)
 * [Parallel::ForkManager](http://search.cpan.org/~dlux/Parallel-ForkManager-0.7.5/ForkManager.pm) from cpan

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 08:51:28 -0000

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 03:57:26 -0000

--- v4
+++ v5
@@ -5,13 +5,13 @@

 ##**Installation**
 Detailed instructions are provided with downloaded documentation for version specific installation. This will require-
-*Perl
-*MODa
-*Java
-*Parallel::ForkManager from cpan
+* [Perl](http://www.activestate.com/activeperl)
+* [MODa](http://prix.hanyang.ac.kr/download/moda.jsp)
+* [Java](https://www.java.com/en/download/)
+* [Parallel::ForkManager](http://search.cpan.org/~dlux/Parallel-ForkManager-0.7.5/ForkManager.pm) from cpan

-##**Documentation
-Docmentation can be found [here](/documentation) or with the downloaded software.
+##**Documentation**
+Docmentation can be found [here](https://sourceforge.net/p/modst/wiki/documentation/) or with the downloaded software.

 ##**Help**
 For any help, please email amit.yadav@thsti.res.in, suruchi@thsti.res.in or post in our [support](https://sourceforge.net/projects/modst/support) forum.

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 03:17:12 -0000

--- v3
+++ v4
@@ -1,4 +1,18 @@
+#**ModST Introduction**
 Welcome to ModST (pronounced "modest") pipeline for Blind PTM searches using the [MODa](http://prix.hanyang.ac.kr/download/moda.jsp) tool.

 ModST can be downloaded from [here](https://sourceforge.net/projects/modst/files/?source=navbar). Please find the latest version and download from the above link.

+##**Installation**
+Detailed instructions are provided with downloaded documentation for version specific installation. This will require-
+*Perl
+*MODa
+*Java
+*Parallel::ForkManager from cpan
+
+##**Documentation
+Docmentation can be found [here](/documentation) or with the downloaded software.
+
+##**Help**
+For any help, please email amit.yadav@thsti.res.in, suruchi@thsti.res.in or post in our [support](https://sourceforge.net/projects/modst/support) forum.
+For Bug reports, use the [ticket](https://sourceforge.net/p/modst/tickets/) system.

Home modified by Suruchi Aggarwal

Suruchi Aggarwal — Tue, 01 Nov 2016 03:08:25 -0000

--- v2
+++ v3
@@ -1,4 +1,4 @@
-Welcome to ModST (pronounced "modest") pipeline for Blind PTM searches using the MODa tool.
+Welcome to ModST (pronounced "modest") pipeline for Blind PTM searches using the [MODa](http://prix.hanyang.ac.kr/download/moda.jsp) tool.

 ModST can be downloaded from [here](https://sourceforge.net/projects/modst/files/?source=navbar). Please find the latest version and download from the above link.