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MUSCLE is a computer software program for creating multiple alignments of amino acid or nucleotide sequences. It is used to predict protein structure, function, and phylogeny, and to infer evolutionary relationships. MUSCLE is faster than CLUSTAL, especially for larger alignments, and is integrated into several software packages, including DNASTAR's Lasergene software, Geneious, and MacVector. MUSCLE is also available as a web service via the European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute (EBI). The MUSCLE algorithm proceeds in three stages: draft progressive, improved progressive, and refinement. The output of MUSCLE is in aligned FASTA format, which is not very readable for people, so an alignment viewer or script that converts FASTA to a more readable format is required.
| Characteristics | Values |
|---|---|
| Name | MUSCLE (MUltiple Sequence Comparison by Log-Expectation) |
| Use | Creating multiple alignments of amino acid or nucleotide sequences |
| Output format | Aligned FASTA |
| Speed | Emphasizes speed over accuracy in the first stage |
| Stages | Draft progressive, improved progressive, and refinement |
| Availability | DNASTAR's Lasergene software, Geneious, MacVector, Sequencher, MEGA, and UGENE |
| Visualization | Multiple Sequence Alignment Viewer (MSA) |
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What You'll Learn
Muscle alignment and body awareness
Correct body alignment is essential for physical and mental well-being. It involves creating a reflective experience that brings awareness to every corner of our being. The first step is to learn to engage the appropriate muscles to enter, hold, and exit a pose. This involves knowing which muscles to activate and which movements or activities are appropriate.
Physiotherapy can help improve body alignment and muscle control. For instance, certain muscles work to maintain a neutral joint position, which is the position of least stress and strain at a joint. These include the deep neck flexors in the neck, the shoulder blade stabilisers and rotator cuff in the shoulder, the transverse abdominus and multifidis around the lower back, the gluteus medius at the hip, and the vastus medialis at the knee. Physio often targets the recruitment of these muscles to improve functioning and alignment through the spine, the shoulder, the hip, or the knee.
To properly activate your core during training, you can follow these guidelines:
- Free weights should make up most of your resistance training.
- Every exercise should be treated like a core exercise – the core should be working in every single movement from squats to running.
- Consciously activate your core until proper firing patterns become second nature.
- Use breathing to guide your core training; feel the breath fill your entire torso.
Additionally, unhelpful thoughts and beliefs can lead to pain behaviours, which include altered posturing and movement. Therefore, it is important to be mindful of our thoughts and actions. We must aim to normalise movement after an injury and bring awareness to certain posturing, alignment, and thoughts. This may involve strengthening certain muscles or learning to relax others.
Furthermore, core training should focus on improving coordination rather than strength or endurance. Running, for example, provides an opportunity to get in tune with your body and anchor awareness in movement. By maintaining awareness of your centre, you can feel how your extremities, down to your fingers and toes, are connected to your centre through distinct lines of tension.
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Benefits of muscle alignment
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Muscle alignment and physical therapy
Good posture is essential for musculoskeletal health. It is the foundation for efficient movement and body function, ensuring gravity is evenly distributed so muscles and joints work optimally. Poor posture can lead to temporary muscle fatigue and chronic conditions like spinal disc and joint dysfunction. It can also cause neck pain, headaches, and even migraines.
Physical therapists can help correct misalignments and restore normal joint function by using manual therapy techniques, exercise, and patient education to address different problems that cause pain or limitations. Therapists use spinal manipulation and other manual therapy techniques to realign the spine back to its normal position, thereby relieving pain. Other treatments can include therapeutic exercise, massages, and treatments based on heat or cold stimuli, such as heat baths, warm mud packs, cold lamps, and ultrasound.
Myoskeletal alignment technique (MAT) is a form of manual therapy that uses scientific evidence about the body and brain to inform the practitioner's approach to musculoskeletal problems. MAT relies on strategic deep tissue and muscle activation techniques for posture correction and pain relief. Massage therapists help the client's brain correct the underlying causes of pain and discomfort. MAT can relieve chronic pain, release trapped nerves from tight muscles, correct atrophy and weakness, address breathing disorders, and improve sleep.
Before applying manual therapy and exercise-based treatments, it is essential to review the major postural muscles and joints and understand their roles and interrelationships. This foundational knowledge assists in effectively managing existing musculoskeletal conditions and plays a crucial role in preventing injuries and enhancing overall physical health.
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Muscle alignment and posture
Good posture is essential for supporting good health. It can help prevent excess strain on your joints, muscles and spine, thereby reducing pain and the likelihood of injury. It can also boost your productivity and mood, as well as help you use your muscles more efficiently.
To check your posture, you can perform the ""wall test": Stand so that the back of your head, your shoulder blades and your buttocks touch a wall, and your heels are 2 to 4 inches away from the wall. Put a flat hand behind your lower back. If your posture is correct, you should be able to just barely slide your hand between your lower back and the wall, indicating a correct lower back curve. If there is too much space behind your lower back, draw your belly button toward your spine to flatten the curve in your back and gently bring your lower back closer to the wall. If there is too little space, arch your back slightly so that your hand can slide behind you.
Posture is a highly individual and dynamic aspect of human physiology. It is about how your body adapts and interacts with different situations, rather than a fixed 'correct' or 'incorrect' state. However, there are some general guidelines for proper body alignment. For example, in a plumb line assessment, the ideal alignment is a vertical line that aligns the earlobe, shoulder, hip, knee, and ankle when viewed from the side. This alignment reflects a balanced distribution of forces across the joints, indicating efficient biomechanical functioning. Weight should also be evenly distributed across both feet, which is crucial for maintaining proper posture and ensuring muscular symmetry.
The erector spinae muscles, which run along the spine, are essential for maintaining an upright posture and resisting the forces of gravity. They provide critical stabilisation during spinal extension and prevent lumbar flexion. The rectus abdominis and oblique abdominal muscles also play a significant role in trunk stability and balance, providing anterior and lateral support to the spine. They are integral in controlling the pelvis's tilt and the lumbar spine's curvature. The gluteus maximus, as the primary muscle in hip extension, is vital for stabilising the pelvis during standing and walking. It counteracts the pelvis's forward tilt and helps maintain the alignment of the lower extremities. The hamstrings are also involved in hip extension and knee flexion, playing a crucial role in postural alignment by balancing the forces exerted by the quadriceps and maintaining the pelvis's neutral position.
To improve your posture, it is important to stay active. Any kind of exercise can help, but yoga, tai chi, and other classes that focus on body awareness can be especially beneficial. It is also a good idea to do core-strengthening exercises and maintain a healthy weight, as extra weight can weaken abdominal muscles and cause problems for the pelvis and spine. Wearing comfortable, low-heeled shoes is important, as high heels can affect your balance and force you to walk differently, putting more stress on your muscles and harming your posture. It is also essential to ensure that your work surfaces are at a comfortable height, whether you are sitting in front of a computer, cooking, or eating. Engaging your core during strenuous activities and breathing out as you lift can help stabilise your spine.
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Muscle alignment and sports performance
Muscle alignment is critical to sports performance. When your body is in its ideal state, your joints and muscles are positioned for maximum function. However, when your muscles are not aligned correctly, your joints will not function optimally, and you may experience pain and faulty movement patterns.
Biomechanical alignment is the ideal state of the body, where joints and muscles work together harmoniously to produce fluid and efficient movements. When your muscles are properly aligned, they can function without excess stress, and you will be able to move with ease and efficiency. This is crucial in sports, where even small gains in efficiency can make a significant difference in performance.
Poor muscle alignment can lead to musculoskeletal pain and impaired movement. For example, tight and short muscles can place abnormal forces on your joints, altering your alignment and causing pain. This pain can hinder your performance and limit your ability to train effectively. Additionally, poor alignment can lead to degenerative changes in your joints and muscles over time, further impairing your athletic abilities.
To optimize muscle alignment and enhance sports performance, consider the following:
- Natural Posture: Be mindful of your natural posture, as we are all built differently. Certain physical activities or movements may exacerbate alignment issues, so it's important to be aware of your body's unique alignment.
- Habitual Posture: Avoid remaining in the same posture for extended periods, as this can create changes in your joint position and muscle length, leading to faulty movement patterns and pain. Take breaks, move around, and stretch to prevent these issues.
- Flexibility: Tight and short muscles can impact your alignment, so focus on maintaining or improving your flexibility through stretching and mobility exercises.
- Physical Therapy: If you experience pain or difficulty with movement, seek the help of a physical therapist. They can perform a biomechanical assessment and develop a treatment program to improve your alignment and alleviate pain. Techniques such as Postural Restoration® exercises can help correct asymmetries and improve your sports performance.
By prioritizing muscle alignment through awareness of your natural and habitual postures, maintaining flexibility, and seeking professional help when needed, you can enhance your sports performance, prevent injuries, and optimize your athletic potential.
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Frequently asked questions
MUltiple Sequence Comparison by Log-Expectation (MUSCLE) is a computer software for multiple sequence alignment of protein and nucleotide sequences. It is licensed as public domain.
MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. It has three stages: the draft progressive, improved progressive, and refinement stage. In the first stage, the algorithm produces a multiple alignment, emphasizing speed over accuracy.
MUSCLE will create a file containing the alignment. By default, the output is created in "aligned FASTA" format. This format is not very readable for people, so to look at the alignment you will want an alignment viewer such as Belvu, or a script that converts FASTA to a more readable format.
