Recent changes to User Manual

User Manual modified by Congting Ye

Congting Ye — Tue, 25 Apr 2017 05:37:18 -0000

--- v15
+++ v16
@@ -26,9 +26,9 @@

 
 ### 3. How to install detectMITE?
-\[1]. Download and unzip our source codes - 'detectMITE.20170331.tar.gz'
+\[1]. Download and unzip our source codes - 'detectMITE.20170425.tar.gz'

-After you download and unzip our source codes ('detectMITE.20170331.tar.gz'), you will see a folder named detectMITE, where all source codes and relevant documents are located.
+After you download and unzip our source codes ('detectMITE.20170425.tar.gz'), you will see a folder named detectMITE, where all source codes and relevant documents are located.

 \[2]. Download and install software required by detectMITE

User Manual modified by Congting Ye

Congting Ye — Fri, 31 Mar 2017 07:54:19 -0000

--- v14
+++ v15
@@ -26,9 +26,9 @@

 
 ### 3. How to install detectMITE?
-\[1]. Download and unzip our source codes - 'detectMITE.20150603.7z'
+\[1]. Download and unzip our source codes - 'detectMITE.20170331.tar.gz'

-After you download and unzip our source codes ('detectMITE.20150603.7z'), you will see a folder named detectMITE, where all source codes and relevant documents are located.
+After you download and unzip our source codes ('detectMITE.20170331.tar.gz'), you will see a folder named detectMITE, where all source codes and relevant documents are located.

 \[2]. Download and install software required by detectMITE

User Manual modified by Congting Ye

Congting Ye — Mon, 02 Jan 2017 03:06:10 -0000

--- v13
+++ v14
@@ -111,6 +111,8 @@
     The description line of each representative sequence (e.g., chr06|2367817|2367964|10|2|109) has the following explanation: 
 \>ChromosomeName|GenomicStartPosition|GenomicStopPosition|TIR_Length|TSD_Length|CopyNumber.

+**Please notice that the TIR length is computed with at most 1 tolerated mismatch. The actual TIR length may be longer than the specified with looser limitations.**
+
 \[2]. MITE families are placed in the file **'genome_name.miteSet.fasta'** in the folder './detectMITE'. And each family are seperated by dot line.
     The description line of each MITE sequence (e.g., >chr06|2367817|2367964|10|2) has the following explanation: 
 \>ChromosomeName|GenomicStartPosition|GenomicStopPosition|TIR_Length|TSD_Length.

User Manual modified by Congting Ye

Congting Ye — Mon, 02 Jan 2017 02:41:46 -0000

--- v12
+++ v13
@@ -108,12 +108,12 @@
 ### 6. Outputs of detectMITE

 \[1]. MITE representative sequences of each family are placed in the file **'genome_name.mite.fasta'** in the folder './detectMITE'.
-    The description line of each representative sequence (e.g., >6|2367817|2367964|2|109) has the following explanation: 
-\>Chromosome|GenomicStartPosition| GenomicStopPosition |TSD_Length|CopyNumber.
+    The description line of each representative sequence (e.g., chr06|2367817|2367964|10|2|109) has the following explanation: 
+\>ChromosomeName|GenomicStartPosition|GenomicStopPosition|TIR_Length|TSD_Length|CopyNumber.

 \[2]. MITE families are placed in the file **'genome_name.miteSet.fasta'** in the folder './detectMITE'. And each family are seperated by dot line.
-    The description line of each MITE sequence (e.g., >6|2367817|2367964|2) has the following explanation: 
-\>Chromosome|GenomicStartPosition| GenomicStopPosition |TSD_Length.
+    The description line of each MITE sequence (e.g., >chr06|2367817|2367964|10|2) has the following explanation: 
+\>ChromosomeName|GenomicStartPosition|GenomicStopPosition|TIR_Length|TSD_Length.

 \[3]. Files in the folder './detectMITE/result/' are temporary files generated during the program running, they could be deleted.

User Manual modified by Congting Ye

Congting Ye — Sun, 31 Jan 2016 05:52:21 -0000

--- v11
+++ v12
@@ -122,7 +122,7 @@
 
 ### 7. Update history

-To see the update history, go to https://sourceforge.net/p/detectmite/wiki/UpdateHistory/
+To see the details of update history, go to https://sourceforge.net/p/detectmite/wiki/UpdateHistory/

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User Manual modified by Congting Ye

Congting Ye — Sun, 31 Jan 2016 05:51:13 -0000

--- v10
+++ v11
@@ -8,6 +8,7 @@
 4. [How to run detectMITE?](#jump4)
 5. [Parameters for detectMITE](#jump5)
 6. [Outputs of detectMITE](#jump6)
+7. [Update history](#jump7)

 
 ### 1. What is detectMITE?
@@ -118,5 +119,12 @@

 [↑Back To Top](#jump0)

+
+### 7. Update history 
+
+To see the update history, go to https://sourceforge.net/p/detectmite/wiki/UpdateHistory/
+
+[↑Back To Top](#jump0)
+
 [[members limit=20]]
 [[download_button]]

User Manual modified by Congting Ye

Congting Ye — Tue, 19 Jan 2016 06:27:06 -0000

--- v9
+++ v10
@@ -3,24 +3,28 @@

 ### Table of Contents
 1. [What is detectMITE?](#jump1)
-2. [How to install detectMITE?](#jump2)
-3. [How to run detectMITE?](#jump3)
-4. [Parameters for detectMITE](#jump4)
-5. [Outputs of detectMITE](#jump5)
+2. [How to cite detectMITE?](#jump2)
+3. [How to install detectMITE?](#jump3)
+4. [How to run detectMITE?](#jump4)
+5. [Parameters for detectMITE](#jump5)
+6. [Outputs of detectMITE](#jump6)

 
 ### 1. What is detectMITE?
 ***detectMITE*** is a MATLAB-based tool for detecting miniature inverted repeat transposable elements (MITEs) from genomes. This software is an open-source tool that follows specifications on website (<http: creativecommons.org="" licenses="" by-nc-sa="" 3.0=""/>).
 If you have any question or comment, please contact with Dr. Chun Liang (<liangc@miamioh.edu>).

-**Citation:** 
+[↑Back To Top](#jump0)
+
+
+### 2. How to cite detectMITE?
 [1]. [Ye C, Ji G, Liang C (2016) *detectMITE*: A novel approach to detect miniature inverted repeattransposable elements in genomes. ***Sci. Rep.*** 6, 19688](http://www.nature.com/articles/srep19688)
 [2]. [Ye C, Ji G, Li L, Liang C (2014) *detectIR*: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation.*** PLoS ONE*** 9(11): e113349.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349)

 [↑Back To Top](#jump0)

-
-### 2. How to install detectMITE?
+
+### 3. How to install detectMITE?
 \[1]. Download and unzip our source codes - 'detectMITE.20150603.7z'

 After you download and unzip our source codes ('detectMITE.20150603.7z'), you will see a folder named detectMITE, where all source codes and relevant documents are located.
@@ -41,8 +45,8 @@

 [↑Back To Top](#jump0)

-
-### 3. How to run detectMITE?
+
+### 4. How to run detectMITE?

 \[1]. To run detectMITE, you shoule make sure the MATLAB environment is installed.  
 \[2]. After opening the MATLAB, change the MATLAB's **Working Path** to the path where detectMITE is installed (e.g., './detectMITE').
@@ -62,8 +66,8 @@

 [↑Back To Top](#jump0)

-
-### 4. Parameters for detectMITE
+
+### 5. Parameters for detectMITE
 ##### Necessary parameters:

 ~~~~
@@ -99,8 +103,8 @@

 [↑Back To Top](#jump0)

-
-### 5. Outputs of detectMITE
+
+### 6. Outputs of detectMITE

 \[1]. MITE representative sequences of each family are placed in the file **'genome_name.mite.fasta'** in the folder './detectMITE'.
     The description line of each representative sequence (e.g., >6|2367817|2367964|2|109) has the following explanation:

User Manual modified by Congting Ye

Congting Ye — Tue, 19 Jan 2016 02:25:37 -0000

--- v8
+++ v9
@@ -14,8 +14,8 @@
 If you have any question or comment, please contact with Dr. Chun Liang (<liangc@miamioh.edu>).

 **Citation:** 
-**I**. [Ye C, Ji G, Liang C (2016) *detectMITE*: A novel approach to detect miniature inverted repeattransposable elements in genomes. ***Sci. Rep.*** 6, 19688](http://www.nature.com/articles/srep19688)
-**II**. [Ye C, Ji G, Li L, Liang C (2014) *detectIR*: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation.*** PLoS ONE*** 9(11): e113349.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349)
+[1]. [Ye C, Ji G, Liang C (2016) *detectMITE*: A novel approach to detect miniature inverted repeattransposable elements in genomes. ***Sci. Rep.*** 6, 19688](http://www.nature.com/articles/srep19688)
+[2]. [Ye C, Ji G, Li L, Liang C (2014) *detectIR*: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation.*** PLoS ONE*** 9(11): e113349.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349)

 [↑Back To Top](#jump0)

User Manual modified by Congting Ye

Congting Ye — Tue, 19 Jan 2016 02:24:21 -0000

--- v7
+++ v8
@@ -14,8 +14,8 @@
 If you have any question or comment, please contact with Dr. Chun Liang (<liangc@miamioh.edu>).

 **Citation:** 
-[Ye C, Ji G, Liang C (2016) *detectMITE*: A novel approach to detect miniature inverted repeattransposable elements in genomes. ***Sci. Rep.*** 6, 19688](http://www.nature.com/articles/srep19688)
-[Ye C, Ji G, Li L, Liang C (2014) *detectIR*: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation.*** PLoS ONE*** 9(11): e113349.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349)
+**I**. [Ye C, Ji G, Liang C (2016) *detectMITE*: A novel approach to detect miniature inverted repeattransposable elements in genomes. ***Sci. Rep.*** 6, 19688](http://www.nature.com/articles/srep19688)
+**II**. [Ye C, Ji G, Li L, Liang C (2014) *detectIR*: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation.*** PLoS ONE*** 9(11): e113349.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349)

 [↑Back To Top](#jump0)

User Manual modified by Congting Ye

Congting Ye — Tue, 19 Jan 2016 02:23:12 -0000

--- v6
+++ v7
@@ -14,8 +14,8 @@
 If you have any question or comment, please contact with Dr. Chun Liang (<liangc@miamioh.edu>).

 **Citation:** 
-[Ye C, Ji G, Liang C (2016) detectMITE: A novel approach to detect miniature inverted repeattransposable elements in genomes. Sci. Rep. 6, 19688](http://www.nature.com/articles/srep19688)
-[Ye C, Ji G, Li L, Liang C (2014) detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation. PLoS ONE 9(11): e113349.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349)
+[Ye C, Ji G, Liang C (2016) *detectMITE*: A novel approach to detect miniature inverted repeattransposable elements in genomes. ***Sci. Rep.*** 6, 19688](http://www.nature.com/articles/srep19688)
+[Ye C, Ji G, Li L, Liang C (2014) *detectIR*: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation.*** PLoS ONE*** 9(11): e113349.](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113349)

 [↑Back To Top](#jump0)