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About FASTA - Tranche Module

ProteomeCommons.org has created a special software module for use with the Tranche tool. This page describes how it is to be installed and used.

FASTA

FASTA Module in Tranche


How To Install

  1. Launch the Tranche Tool
  2. Open the Advanced Tools menu at the top of the tool.
  3. Click the Open Module Manager menu item.
  4. Once the Module Manager opens, scroll down the table that is under the title Install modules from server until you see a module named FASTA Module (See Figure 1). Click this row of the table, then click the button named Install Selected Module from Server. You will be notified of success or failure to install.
  5. You should now see the FASTA Module added to the table under the title Installed modules. You have successfully installed the module.
Figure 1

What It Does

This module contains several useful functions for FASTA files: concatenation, FASTA format conversion, and reversing protein sequences.

Concatenate. All of the files that are added to the list of input files will be concatenated into a single output file. The input files can be taken from your local network or they can be references to files on Tranche (give the Tranche hash of the file). The Tranche files will be downloaded in the background before concatenation begins. There is no limit to the number of files, nor to the size of the files.

Convert. The concatenated output file will be of a FASTA format of your choosing. These possible formats are limited to the FASTA writers that are currently available within the ProteomeCommons.org IO Framework. None of the original files will be altered. Note that Generic FASTA (.fasta) format will leave the format as it is for each protein sequence entry.

Reverse (Optional). If selected, each input file will be concatenated as normal, but also concatenated will be the same file with the protein sequences of each entry reversed and a reversion signifier (default is "_REVERSED") added to the accession for that entry. You can change the reverse signifier to anything you want. Note that with this operation selected, the process will take twice as long and will result in a file that is twice as large than if it had not been reversed.


How To Use It

This module is not automatically available. Make sure you've installed the module first.

Open the FASTA Module.

There are two ways to open the FASTA Module: directly from the Advanced Tools menu, or from within a project that contains a FASTA file.

Opening the module from the Advanced Tools menu is the easiest way to get to the tool. Select the Open FASTA Module option from the Advanced Tools menu. The FASTA Module frame will open.

From here, you can continue to browse the Tranche network for FASTA files, getting their Tranche hashes and adding those as input files.
Figure 2

You can also open the FASTA Module while viewing the contents of a project. Once you find a find a .fasta file or set of files and select them, the Open FASTA Module option in the left menu will become available.

Clicking this will open the FASTA Module with the selected files already loaded (See Figure 4).
Figure 3

Figure 4

Configure Your Output.

The Input Files are the set of FASTA files that you want to concatenate. They are represented here in a table, where each row of the table is a unique input file. Each file is represented with a location, either on your local network or on Tranche, and a FASTA Format. From this table, clicking the FASTA Format of any row will bring up a list of FASTA readers for you to select from.
Figure 5

You can add an input file to the table by clicking the Add option from the Files menu. In the frame that pops up, you can enter either the Tranche hash of the file you want to use or you can use the Select File button to pick which file you want to use.
Figure 6

If you know the format of the file you want to use, please select it from the drop-down list.
Figure 7

The Output Location is the file that is to be created. When selecting a pre-existing file, note that the output from this task will be appended to the end of that existing file.

The Output Format is a drop-down menu of all the available FASTA writers within the ProteomeCommons IO Framework.

Check the Reverse protein sequences box if you also want to concatenate the reversed protein sequence entries of all of the input files.
Figure 8

Click the Concatenate FASTA Files button when you are done configuring your output. A progress bar will appear at the bottom of the frame that will notify you of your progress.
Figure 9


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