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Sequery Manual

Last updated August 8th, 2014

For Sequery version 1.0

Table of Contents

Getting Started 5

Sizes & Sort 8

Length Min= 8

Length Max= 8

Length Distribution 8

Sort by Length 8

Alphabetical Sort 8

ATGC Proportions 8

Extract 9

BarCodeStr= 9

BarCodeStrStart= 9

5’AdptrStr= 9

5’AdptrStrStart= 9

3’AdptrStr= 9

3’AdptrStrStart= 9

Extract>5’[] 13

Select Folder ->[] 13

Save as FASTA -> [] 13

Save as TEXT -> [] 13

Save Window Prefs ->[] 13

Save .idx file ->[] 13

Assorted 13

IntertSeq 13

Getting Started

Sequery v1.0 (Mac OS X Intel) Readme/Installation (July 22, 2011) GWH

Installation:

Copy Sequery.zip file to your desktop. Double click on the icon which will create a folder called Sequery. Drag the folder to the main Applications folder (i.e. /YourHardDrive/Applications, not /YourHardDrive/Users/Whomever/Applications folder). Inside the folder there is the main app (Sequery_v1.0) and a folder called “Prefs”. No other files are installed anywhere. To de-install, just move the Sequery folder to the Trash and Empty Trash. This will completely remove it.

If you like, you can drag the Sequery_v1.0 folder to the dock for easy access. To display the associated Terminal window while running Sequery, see “Enable Console” at the end of this document.

First time Setup:

1) Sequery requires a 3 button mouse. Any old PC mouse will work. The scroll wheel, when depressed, is called the middle mouse button (MMB). If the MMB or RMB are not working, go to the “SequenceAnalyzer” menu -> Preferences… and click on the Mouse tab in the GLUT Preferences pane. Check the “Enable Button Emultion” (with RMB as Control, and MMB as Option), then hit OK.

2) Upon opening Sequery for the first time, the 3 windows may appear small and misplaced. Move and resize the windows (move by LMB click/hold on top bar, resize by LMB click/hold on the bottom right area of each window) to your satisfaction, then in the FileMenu window (has gray background), click on the text on the upper right hand side that say “Save Window Prefs”.

3) Lastly, in the top left of the FileMenu window are 5 slots in which you can save favorite folders. To reset them, MMB click on each of the slots (this will default to your desktop).

Opening a file:

1) When Sequery is opened, it will automatically display the FileMenu window in which folders are displayed on the left, and files within a current folder are display on the right. Files ending in recognizable suffixes (.txt, .fa, .fna, etc) are colored. To open a file, position the mouse over the text listing of the file under “FILES” on the right hand side of the window (it will turn yellow), and click the LMB.

2) To go to a different folder, click on a folder in the left folder column. To go back one level, right click the “CURRENT” directory path near the top.

Display

[pic]

1. Info Area

XX Ranked = number of sequences that include the bar code.

SeqList = Specifies the file number (if there are multiple number of files).

Original Seqs = Number of sequences in the loaded file.

Raw Range = Length Range

Unduplicated =

In Range = Uses Size selected range

Index = Type of file that is currently showing.

2. File Name

T or R= Switches between test and reference sequences

C = Checksum array exists

Yellow Box next to the slot indicates the current library (which routines will be performed on)

3. Sequence Graphic Representation

Nucleotide sequences displayed graphically as a row of colored squares:

Color conversion:

‘A’ = light blue (azure)

‘T’ = purple

‘G’ = green

‘C’ = beige (camel)

‘N’ = gray

Box on the LHS displays an overview of all the sequences in a particular file – or displays a partial list of sequences based on:

- raw listing

- sorted by size

- unique/unduplicated sequences

- extracted sequences

- ranked sequences

The box on the right hand side of the main Sequery window, displays a subset of the sequences at higher detail.

4. Sequence Display

Flexible display of individual sequence data as:

-gene maps (chromosomes)

- 2D geometric displays

- 3D geometric displays

Sizes & Sort

Length Min=

RMB to bring up a slider to set the minimum length of sequences

LMB click to run routine (will use both min and max values)

Sets the minimum length of the sequences

Length Max=

RMB to bring up a slider to set the maximum length of sequences

LMB click to run routine (will use both min and max values)

* the size sorted sequences will be displayed in the overview box (2nd checkbox)

Sets the maximum length of the sequences

Length Distribution

Saves a frequency distribution of lengths in a text file. The value indicates the bin size (use RMB click to bring up slider and adjust).

Sort by Length

Sorts the sequences by length

Alphabetical Sort

Sorts the sequences by nucleotide arrangement alphabetically

ATGC Proportions

Saves the proportions of A, T, G, C & N in a text file.

Extract

BarCodeStr=

Given a two letter bar code, it will identify the sequences with that barcode

BarCodeStrStart=

Sets the range in which to search for the bar code string

5’AdptrStr=

Extracts sequences with the appropriate 5’ adapter sequence (e.g. TAGAAA)

5’AdptrStrStart=

Sets the range to search for the 5’ adapter

3’AdptrStr=

Extracts sequences with the appropriate 3’ adapter sequence (e.g. AAAAA)

3’AdptrStrStart=

Sets the range to search for the 3’ adapter

Extract>5’[]

Loads a number of different file types.

Files with valid suffixes include:

.fa loaded as a FASTA file

.fna “ “

.fq loaded as a FASTQ file

.idx allows fast loading of a sequence based on a previously generated index (idx) file

Text files (.txt) can be loaded a number of different ways:

Press ‘1’, ‘2’, or ‘3’ in the FileMenu window to load text files arranged as:

1: INFO

2: INFO | SEQUENCE

3:

INFO | SEQ | DUPLCIATES

Press ‘g’

- loads in a genemap for a particular sequence (usually a chromosome)

- INFO | CODE | START | END";

Press ‘x’

- will create an index file of a list of sequences. Note – the index file will not be displayed in the overview window…. (I think)

Save as FASTA -> []

Saves the file as a fasta formatted file.

If sequences were extracted, two variables are concatenated to the information line as “exLength=xxx” – original length of the sequence before extraction

“exDups=xxx” – number of duplicates of a particular sequence (if saving unduplicated lists)

Save as TEXT -> []

Saves the file as a text file. Defaults to INFO | SEQ | DUPLCIATES

Save .idx file ->[]

Indexes fasta files to be compressed.

Enable Console

In Finder, go to Applications -> Sequery. Right click SequenceAnalyzer -> Show Package Contents. Contents -> MacOS -> Drag new SequenceAnalyzer icon to Applications.

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2. File Name

1. Info Area

4. Sequence Display

3. Sequence Graph

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