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– Extension Doctor scans loaded FAST or tab delimited sequences and produces an extension file. – You have to specify the FAST version you want to clean (Fasta or FASTQ) and the extension file name you want to create. – You can also append the original sequence of the current FAST file and the extension file name that you will save it. – This option is useful if you are analyzing several sequences at the same time. – By default extension files are saved with an.ext file extension. – You can change this option and specify the extension file name that you want to save. – Extension Doctor works on Windows operating systems and it was tested only with the.fasta or.fqt sequence formats. FileDoctor is an easy to use tool for the extraction of sequences from the header. FileDoctor supports all the common formats including FASTA and FASTQ. FileDoctor Description: – FileDoctor supports several common formats including FASTA, FASTQ, FAST5 and SAM. – It has a complete set of options and advanced features to generate outputs in the specified format. – It supports different type of headers, including gzip and bzip2 compressed. – It supports opening compressed formats, such as gzip and bzip2. – It allows you to automatically uncompress the file. – FileDoctor can generate the output in several formats, including FASTA, FASTQ, FAST5 and SAM. – You can generate a CSV output in several formats, including FASTA, FASTQ, FAST5 and SAM. – The number of sequences per line can be manually or automatically adjusted. – You can generate a text file with the same sequence for each line. – By default, your output files are saved with the extension.out (for example:.out.fasa,.out.fqt,.out.fast5,.out.sam, etc.). – You can change the extension of your output files. – FileDoctor can be run in command prompt (type the command in a cmd window) or with a batch file. – You can run the application in batch mode so that multiple input files are processed at the same time. – You can generate a ZIP archive that includes several output files. SpoolDoctor is a simple and easy to use tool for the extraction of sequences from the header. SpoolDoctor

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1. You can choose whether the sequence is a FASTQ file, a FASTA file or a tab-delimited file. 2. Nucleotide sequences can be loaded in a single window. 3. The program scans automatically the sequences in the loaded file, creating a data structure that represents the sequence. 4. The data structure is very similar to the one created by bwa-mem. 5. You can edit the file data structure in the extension tool window. 6. You can save and load data structure files. 7. You can view the summary of all data generated in a data structure, from more than 100s of sequences. Full Width Half Maximum Full Width Half Maximum is a handy tool that aims to measure the width of a peak (or other type of function) in a specific time range. It works by allowing you to select a region of a plot in the graphic window, and by clicking on the corresponding button you are able to add to the graph a numerical value corresponding to the Full Width Half Maximum value of the selected data points. Smart Dynamic Plotter The Smart Dynamic Plotter is a nice simple graphical user interface for plotting time series of data in real time. It allows you to plot an oscillator model (that is, a mathematical function that approximates the behaviour of your system) and monitor the time evolution of several variables (real-time, user defined). Sammy The SAMmy application, is a powerful desktop application that allows users to work with SAM and BAM files. The application works directly with files and is able to read and write them in common formats such as SAM and BAM. The application has been developed with python and is available in the following platforms: Linux, Mac OS and Windows. Gnuplot Gnuplot is a software plotting package for the X Window System. It allows the user to create very high quality publication quality graphics, using a simple and intuitive command language. It is able to read and write any kind of X-windows output, from Postscript or PDF to SVG. RSEQ RSEQ is an acronym for the complete sequencing and validation of RNA from single cells. A key element of this tool is that it integrates a fast and efficient library preparation kit to obtain total RNA from single cells that allows: i) a better quantification of each transcript, ii) a better resolution of transcripts at different cellular levels, and iii a86638bb04

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Extension Doctor is a simple and easy to use program that aims to help users who need to clean nucleotide sequence data on the fly. The application is able to scan a loaded FAST or tab delimited sequence file and it will remove automatically any nucleotides that are identical with each other and placed at the 3′ and 5′ ends of the target sequence. Read more File Fusion is a simple and easy to use utility that aims to help you merge multiple files of any type into a single single one. The application is very easy to use and it does not need to be installed because it is available as an executable that is easy to run. Extension Doctor Description: File Fusion is a simple and easy to use utility that aims to help you merge multiple files of any type into a single single one. The application is very easy to use and it does not need to be installed because it is available as an executable that is easy to run. Read more NCBI BLAST is a free tool that aims to help users to quickly scan a nucleotide sequence database for sequences with matches against an input sequence or a user-specified sequence. The application is easy to use and it does not require a previous installation because it runs on a simple desktop icon and all the necessary data are loaded automatically in a temporary file. Extension Doctor Description: NCBI BLAST is a free tool that aims to help users to quickly scan a nucleotide sequence database for sequences with matches against an input sequence or a user-specified sequence. The application is easy to use and it does not require a previous installation because it runs on a simple desktop icon and all the necessary data are loaded automatically in a temporary file. Read more My Friend is a simple and easy to use tool that aims to help users to scan a nucleotide sequence database to find sequences that share at least 90% identity with a user specified sequence. The application is very easy to use and it does not require a previous installation because it runs on a simple desktop icon and all the necessary data are loaded automatically in a temporary file. Extension Doctor Description: My Friend is a simple and easy to use tool that aims to help users to scan a nucleotide sequence database to find sequences that share at least 90% identity with a user specified sequence. The application is very easy to use and it does not require a previous installation because it runs on a simple desktop icon and all the necessary data are loaded automatically

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The main window of the application includes the following features: – Load Sequence – Clean Sequence – Statistics – Save Sequence – Show/hide warnings To use the application, launch it from the Start menu, locate the launch menu item and select “Extension Doctor”, then follow the on-screen instructions. The cleanup feature works by checking for identical nucleotides at the 3′ and 5′ ends of the target sequence. In order to clean the sequence data, Extension Doctor uses the 3′-5′-end format for nucleotide strings, which is a data format specifically designed to represent a nucleotide string like “ATGTGGA”. This format allows Extension Doctor to delete nucleotides that are identical and to determine how far from the 3′ and 5′ ends nucleotides are located. Some basic steps to clean nucleotide sequence data: – The option “Load Sequence” is used to load an input sequence file into Extension Doctor. The extension.ini file should be provided, containing the name of the input sequence file. – Once the sequence file is loaded, the user can select the sequence region and the format to analyze (FAST or tab delimited). – When the sequence is ready, the user can select “Clean Sequence” from the menu. – The application will output an output sequence file and a file showing the statistics of the cleaned sequence, the original sequence and the amount of cleaned nucleotides. Sample data: The following sequence file was created with the Sequence Generator tool from the NCBI website: input_sequence.fastq Input Sequence: >gATTCTATCTCCCTATCTCACCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTGTGGA The following sequence was obtained from the Sequences.txt file: ACAGATGGAACAGATGGTGTGAGGTAGGTAGGTAGGTATGGATAGGAATAAGAGTGAGATGAACTGTGAT ATCGTAGTATGTGTGTGGATGTTAGGTATGTGTGTGTATGTGGAGGTAGGTAGGTAGGATGGTATAGGAT ATCAGATGGAATCCAGATGCTAGTGAGAGGTAGGAGAGGTGGTAGTTTATGGGATGAGGATGCAGAACAG TGTGGTATGTAGAGAGGTGGTGTAGGATGATGGTGGTGTGGTGTGTTTATGGTGGAGTATGATGGTGGG GTAGGTAGGTAGGTAGGTATATAGGATGTTTGGTGGAGGAGGTGGTGTGAAAGTGAGAGTGTGTGGTAG GTGTGT

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Processor: Intel Core 2 Duo @ 2.0 GHz or AMD Phenom X3 @ 2.8 GHz or better. Memory: 1 GB RAM. Graphics: OpenGL 2.1. DirectX: Version 9.0. Hard Disk Space: 1 GB free space. Network: Broadband Internet connection. Play As: Single-player or Co-op with up to 4 players. Download:

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