.SAM File Extension

LMHOSTS Sample File

Developer	Microsoft
Popularity	Average rating 3.9 / 5. Vote count: 28
Category	Text Files
Format	.SAM
Cross Platform	Update Soon

What is an SAM file?

SAM, which stands for Sequence Alignment/Map, is a widely used file format in bioinformatics and genomics. It is primarily employed to store data related to the alignment of DNA or protein sequences. SAM files play a crucial role in organizing and analyzing high-throughput sequencing data generated from various sequencing technologies, such as Illumina, PacBio, and Oxford Nanopore.

More Information.

The SAM file format was created as an evolution of its predecessor, the Sequence Alignment/Map (SAM) format. The earlier SAM format had limitations, including limited compatibility with large datasets and slower parsing times. SAMtools, an open-source suite of programs developed by Heng Li, introduced the Binary Alignment/Map (BAM) format, which was a more efficient binary representation of SAM files. SAM files, however, remained in use due to their human-readable nature, making them easier to inspect and manipulate directly.

Origin Of This File.

The SAM file format was first introduced to the bioinformatics community in 2009 as a standardized way to store sequence alignment data. It was developed in response to the growing need for a common format that could accommodate the vast amount of sequencing data being generated in research and clinical applications.

File Structure Technical Specification.

A SAM file consists of header lines and alignment lines, where each alignment line represents the mapping of a read (sequence) to a reference genome. The header contains metadata about the reference genome, read groups, and sequencing platforms used. The alignment lines include fields like read name, reference sequence name, alignment position, mapping quality, and more. The SAM file format is tab-delimited and is well-documented in the SAM specification, making it easy for software developers and researchers to work with.

How to Convert the File?

Windows:

Using Software: Windows offers a wide range of software applications for file conversion. Depending on the file type you want to convert, you can use software like Microsoft Office, Adobe Acrobat, or dedicated conversion tools like Format Factory, HandBrake (for video conversion), or Any Video Converter (for multimedia files).
Online Converters: There are many online file conversion websites and services available. Simply search for a relevant online converter, upload your file, select the desired output format, and initiate the conversion process.

Linux:

Command Line: Linux offers powerful command-line tools for file conversion. For instance, you can use ‘ffmpeg’ for video and audio conversion, ‘ImageMagick’ for image conversion, and ‘pdftotext’ or ‘pdftohtml’ for PDF conversions. Use the terminal and relevant command syntax to convert your files.
GUI Tools: Linux also has graphical user interface (GUI) software for file conversion. Tools like LibreOffice, GIMP (for images), and HandBrake (for videos) provide user-friendly interfaces for conversion tasks.

macOS (Mac):

Built-in Tools: macOS includes several built-in tools for file conversion. For example, you can use the Preview app to convert images and PDFs, or the macOS Mail app to convert email attachments to different formats.
Third-Party Apps: Similar to Windows, you can install third-party applications like Adobe Acrobat, HandBrake, or Format Factory to handle various types of file conversion.

Android:

Dedicated Apps: Android provides a plethora of dedicated apps for file conversion. Depending on the file type, you can install apps like “Total Converter,” “MP3 Video Converter,” or “Image to PDF Converter” from the Google Play Store. These apps often support multiple input and output formats.
Online Services: Android also supports online file conversion services via web browsers. You can visit websites like Online-Convert.com or Zamzar from your Android device, upload the file, and select the desired output format for conversion.

iOS (iPhone/iPad):

App Store: iOS users can search the App Store for dedicated file conversion apps. For instance, you can use apps like “Documents by Readdle” or “File Converter” to convert files on your iPhone or iPad. These apps often support various formats.
Online Services: iOS devices can access online conversion services through web browsers, similar to Android. You can visit websites like Online-Convert.com or CloudConvert via Safari, upload your file, and choose the desired output format for conversion.

Advantages And Disadvantages.

Advantages

Human-Readable: SAM files are plain text and can be easily inspected and edited with a text editor, making them accessible to researchers for manual examination.
Flexibility: SAM files can store a wide range of information related to sequence alignment, making them versatile for various analysis needs.
Compatibility: SAM files can be converted to BAM format and vice versa, allowing for efficient storage and analysis.
Standardization: SAM format has become a standard in the field of genomics, ensuring interoperability across different software and platforms.

Disadvantages

Large File Size: SAM files can be quite large, especially for projects with extensive sequencing data, which may lead to storage and processing challenges.
Parsing Complexity: Parsing SAM files can be computationally intensive, particularly for large datasets, due to their text-based format.
Limited Platform Support: While SAM files can be opened and processed using various bioinformatics tools, they may not be natively supported by all software applications.

How to Open SAM?

Open In Windows

In Windows, .SAM files are typically not meant to be opened directly. They are system files used by the operating system for authentication and user management. Interacting with .SAM files should be done through system utilities and security management tools.

Open In Linux

Linux systems do not use .SAM files for user authentication. Instead, Linux uses different file formats and mechanisms for storing user account information, such as /etc/passwd and /etc/shadow files. To manage user accounts in Linux, you should use standard Linux utilities like ‘useradd’ and ‘passwd.’

Open In MAC

Open In Android

Android, being a Linux-based operating system, follows Linux conventions for user account management. There are no .SAM files on Android devices. To manage user accounts on Android, you can use the built-in user management tools or third-party apps.

Open In IOS

iOS, the operating system for Apple’s mobile devices, does not use .SAM files either. User account management on iOS devices is handled through the iOS interface and settings. There is no need to interact with .SAM files on iOS devices.

Open in Others

Other operating systems and applications may have their own unique file formats and methods for user account management. It’s essential to consult the documentation specific to the system or application you are working with to understand how to interact with user account data effectively.