SEQEDITOR - USAGE


2.1 - TOP MENU

The Top menu provides access to the sequence browser and to other interfaces through which the fasta manager tasks can be executed. This allows the user to process and analyze all the sequences included in one or multiple fasta files simultaneously without the need of open the files separately.


Figure 2

Figure 2: Main menu of the SeqEditor Application


TOP MENU: DIRECTORY

TOP MENU: FILE

TOP MENU: SEQUENCES


Figure 3

Figure 3: Orientation and Geometry windows layout. Left) The orientation dialog allows the user to change the orientation of the sequences to their reverse, complement or reverse complement sequences; Right) The geometry dialog allows the user to change sequences from DNA to RNA or vice versa.



Figure 4

Figure 4: Filter and Sort windows. Left) The ”filter” dialog allows the user to filter sequences by given search terms and matching criteria; Right) The ”sort” dialog allows the user to sort sequences either alphanumerically or by a given term in a CSV file.



Figure 5

Figure 5: Split sequences dialog. The tool allows the user to: i) Split the sequences of your files by sequence names introducing list of names or a text file, including them in a select and match mode (exact or partial); ii) split in subsets of up to a given number of sequences introducing the number of sequences per file; iii) Split by sequence length introducing the desired length and select the comparison type: equal to selected length, greater than selected length or lower than selected length; iv) split scaffolds into contigs considering gap regions introducing sequence size and, if it is the case, a padding value.


Figure 6

Figure 6: Remove/masks sequences from your fasta files. Using this parameter, the function will remove every sequence which is composed by a 100% of N.


TOP MENU: ORFs:


TOP MENU: MOTIFS


TOP MENU: STATISTICS

HELP:


2.2 - SEQUENCE BROWSER MENU

The SEQUENCE BROWSER is a GUI that allows the users to navigate, edit, and analyze sequences under visual control. It automatically opens when opening a fasta file by clicking on the top menu -> File -> Open File. It can also be called by right-clicking on an input sequence file in the specified directory. The menu of the sequence browser in the latest version of SeqEditor (v2.1.6) compiles all the different functions of the sequence browser and two new implementations that interact with the browser. These are a GTF/GFF viewer tool that allows the user to mine and export sequence features using specific annotations of GTF/GFF files; and a set of tools for PCR primer design based on an interface adaptation of two CLI tools - Primer3 (Untergasser et al. 2012) and PrimerPooler (Brown, et al. 2017). These tools include newly optimized and validated search processes for the design of multiplex and target-specific primers. The screen of the Sequence Browser is interactive, allowing users to select, copy, cut and paste sequence traits by right-clicking on the sequence. You can lock or unlock manual sequence editing by selecting Locked/Unlocked in the “Edit” tab of the sequence browser menu.

The graphic capacity of the sequence browser relies on the RAM power of the user's hardware; however, it has been optimized to manage large sequences, such as contigs, scaffolds and chromosomes without experiencing significant slowdown. This means that the users can work with sequences up to 300Gb with only 25Gb of RAM assigned to SeqEditor and will not experiencing any delays in processing times. These sizes efficiently cover the largest chromosomes known to date. Only one sequence is allowed per browser screen. However, when opening a fasta file with multiple sequences, a file summary view is opened at the bottom of the browser summarizing the sequences included in the file. Additional sequences can then be selected and analyzed in other screens of the browser. Lastly, the fasta file summary screen view presents a submenu that includes other tools for the editing and management of the listed sequences.

The Sequence Browser can manage both nucleotide and protein files and can automatically tell them apart. This means that if you create a new nucleotide layout in the sequence browser and try to copy a protein sequence (or viceversa) in it, you will be not allowed to do so.

The sequence browser manages the sequences one by one. If you are interested in managing files with multiple sequences or multiple files, you must use the top menu. The menu of the sequence browser is organized as follows:

Figure 12

Figure 12: Sequence Browser Menu.


BROWSER MENU : Sequences



BROWSER MENU : EDIT



BROWSER MENU : GEOMETRY


BROWSER MENU : ORIENTATION

BROWSER MENU : TRANSLATE


BROWSER MENU : FIND ORFs


BROWSER MENU : FIND MOTIFs


BROWSER MENU : Primers:

SeqEditor implements a set of three tools for singleplex, multiplex PCR primer design and primer pooling powered by an interface adaptation of two CLI tools: Primer3 (Untergasser et al. 2012) and PrimerPooler (Untergasser et al. 2012). This tool also incorporated a newly optimized search process that is based on two algorithms for multiplex and target-specific primer design (Hafez et al. 2020). These three tools (designated as SinglePlexPCR, MultiPlexPCR and PrimerPooler respectively) are organized in three separate interactive interfaces that are accessible through the “Primers” tab of the browser menu.

To provide some examples how to use PrimerPooler, MultiPlexPCR and SinglePlexPCR as well as to validate the new search strategy for multiple species-specific primers, we have prepared a case study tutorial. In this case study, the MultiplexPCR tool use was used the design of multiplex species-specific primers for five Candida species (OPATHY Consortium and T Gabaldon 2019). The target DNA sequences selected for this example were the ribosomal DNA sequences of the five Candida species as retrieved from the NCBI databank (Sayers et al. 2019). This tutorial is available online at the following link: https://gpro.biotechvana.com/tool/seqeditor/candida_target_specific2020.

BROWSER MENU: Annotation

SeqEditor supports the analysis of genomes and transcriptomes that have a reference annotation file (GTF/GFF). Thus, we have incorporated a GTF/GFF viewer that reads the reference annotation file allowing the users to search, filter, and extract sequence features (such as chromosomes, genes, exons or introns) contained in the assembly file using the annotation as a reference.

The GTF/GFF viewer has been tested with several different assemblies and GTF/GFF files available in the Candida Genome Database (Skrzypek et al. 2017), Ensembl (Cunningham et al. 2019) and the NCBI (Sayers et al. 2019), as well as a with a tailor-made GTF file that was created based on the gene prediction generated by the AUGUSTUS 3.3 software (Stanke et al. 2008) for the Sparus aurata genome (Pérez-Sánchez et al. 2019). The GTF/GFF viewer also accepts .bed files and other files in plain format.

The viewer will open when double-clicking on a sequence file in the directory browser or via the “Annotation” tab of the browser menu. The “Annotation” tab will show the following options:


Once the GTF/GFF file is loaded, users will visualize all the data as an annotated grid of rows and columns that will be organized based on the information contained in the annotation file.
Figure 23

Figure 23: View of the sequence browser (top) and the GTF/GFF viewer (bottom) when opened simultaneously. The annotation viewer shows the features (such as gene, exon, CDS, etc.) that are contained in the sequence of interest. The viewer has five additional options for the management of these annotations: i) Filter within columns: Shows/hides the filter option. When the filter option is shown, the user can filter by any of the terms contained in any column displayed in the annotation file. For example, when writing “gene” on the filter section of the Feature column, the annotation viewer will only display those rows that correspond to a gene. ii) Search Features: Searches and checks a feature according to different criteria; III) Save Annotation: Saves, Saves As or Exports (just for rows); iv) Extract sequences: Extract features from the reference sequences through a pop-up dialog; v) Revise Edits: Revises and corrects the features of the coordinates that are affected by the edition of the reference sequence.


The GTF/GFF viewer allows the user to perform different tasks. Some of them can be executed with the mouse while others can be implemented via a menu.
Figure 24

Figure 24: GTF/GFF viewer: mouse-dependent and menu options.







GPRO licensing and Usage           Former versions

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