Understanding Sequence Alignment Algorithms: with Needleman-Wunsch

In this video I will discuss the components of a sequence alignment algorithm, specifically with the Needleman-Wunsch algorithm as an example. Many of these properties will also apply to Smith-Waterman, but not all. Needleman-Wunsch is a global alignment algorith, meaning it aligns the entire sequences to each other, instead of the local alignment provided by Smith-Waterman.

[kaidenwilliams]

I don't often comment on YouTube videos, but this was explained as clearly and succinctly as I could imagine. Thank you for making this video, it helped me out a lot in my understanding of the algorithm.

[biobruh...]

Great video!. Had a tough time understanding Neeldeman-Wunsch, but I got it now. Thanks for the clear and structured explanation!

[Am-ugnp]

I watched like every other video on this topic on youtube, and not 1 other person mentioned the traceback matrix OR that we need to look for gaps in both x and y, for some dumb reason lol. I finally understand thanks to your video

[mattralston]

Really excellent! Succinct and simple to understand. Thanks for mentioning substitutions and affine scoring. That's a nuance that shows real mastery and I like your video!

[Periareion]

This was very helpful. Thank you, Hendrix!

[verinen_runkkari]

Hi! At 9:51 when the video was fastforwarded you were getting into the matrix entry on which the row and column both corresponds to "C". Why was -1 added instead of +1?

[aurel]

Thank you so much. I took bioinformatics, but at Biology level and we lack a lot of Mathematical and Statistics background at my uni - not to mention Informatics. We touch on these options in Blast but for me to learn I need to know how something works at least a bit. A lot of informatics and statistics info is very overwhelming but you put it very succintly so that even I understood.

[alexkesin]

Great video! Explained this super clearly

[nycoshouse]

hello, is there a meaning or applications to use a base 4 system and associate CAGT with 0123 ?

[RowingIsFun]

Good stuff! Thanks for making this video.

[alimudarres]

Also, anyone else running into more complex or unequal lengths of sequences, there can be multiple solutions since your trace back matrix could have branches going multiple paths all giving the same score. Easiest would be to trace a path and read it from top left to bottom right to avoid confusion with where to apply the gap etc

[vitortarghetta]

Awesome! Thanks for the uploading this video!

[busbusvlog]

Thanks a lot! This was very helpful for my studies

[MultiSpiros]

So good explanation !!!! thank you !!!

[Msyoutube]

On the column and row where first A's match why do we pick to go(11.11) right side (2->1)when we can also move downwards on that backtracking matrix?Makes no sense to me..

[halafares]

what if its a semi-global alignment ??? how cam i use this website ??

[qaziacademy]

Sir ur videos are amazing. Please i need ur kind help in Feature extraction. Please help me.

[gschitz]

⥊ 771: 58

0: Good (if not good, then not zero)
0001: Uniqueness

001: Identity
002: Individuality
003: Variability
004: Diversity
005: Tolerance / Inclusion
006: Acceptance
007: Consonance / Harmony
008:
009: Transcendence

01: Awareness
02: Diversion
03: Sensing
04: Love
05: Grace
06: Reasoning
07: Ingenuity
08: Purity
09: Truth Seeking

1: Ethical
2: Problem-Solution
3: Situation
4: Abstraction
5: Expression Concrete
6: Why/Who/When/How/Where/What
7: Information/Code
8: Stability
9: Sanity

10: Network (Good Network, because zero)
11: Justice
12:
13: Death / Fact
14: Cognition
15: Agent
16: Reason
17: Discourse
18: State
19: Discipline / Control

20: Judgement
21: To Solve Problems with Ethics
22: Resistance/Endure Introspection
23: Consideration
24: Humor / Mental State
25: Behavior
26: Motivation
27: Cohesion
28: Dependability
29: Prognostic

30: Liberty Subject Wellness
31: Consent
32: Discernment
33: Response
34: Ideas
35: Showing
36: Option
37: Opinion
38: Decision
39: Optimism

40: Wellness
41: Attention / Idea
42: Critical Thinking
43: Acknowledgment
44: Free Love
45: Plan / Task Force
46: Purpose
47: Perspective
48: Character
49: Ambition

50: Good Expression
51: Manifestation
52: Support
53: Respect
54: Care
55: Peace / War
56: Pointing / Profiling
57: Tell / Counter-Terrorism
58: Invoking / Building
59: Proficiency / To Excel

60: Certainty
61: Identification
62: Qualification / Characterization
63: Inquiring
64: Conjecturing
65: Function / Role
66: Investigation
67: Arguing
68: Indicator
69: Scrutinity

70: Validation
71: Illustration / Knowledge
72: Construct
73: Explanation / Informing
74: Data
75: Materialization
76: Delineation / Instruction
77: Flow / Cadency
78: Share
79: Accountability

80: Personal Soverenity
81: Independency Constancy
82: Resilience
83: Established
84: Autonomy
85: Executing
86: Authority
87: Stream
88: Consistency
89: Boldness

90: Wisdom
91: Assertiveness
92: Science
93: Scrupulousness
94: Integrality
95: Composure
96: Blockchain: ⥊ (TRACE MARKER)
97: Anarchy
98: Veganism
99: Revolution

100: Liberation
101: Space and Time Peer-2-Peer
102: Decentralized Network
103: Financial Revolution
104: Production Revolution
105: Labour Reorganization
106: Needs Evaluation
107: Instruction
108: Personal Sovereignty
109: Resources Availability

110: Frankness
111: Honor
112: Distributed Ledger
113: Privacy
114: Abolitionism
115: Pride
116: Pacifism
119: Mission
120: Harvest
121: To Revolt
122: To Sort Out
125: Differentiate
126: Distinguish
130: Realization
131: Fulfillment
132: Regard
133: Perform
134: Address
135: Execute
136: Obtain
138: To Mark
140: Serenity
141: Idea
144: To Notice
148: Mindfulness
150: Good Character
151: Virtue
155: Honesty
160: Technology
161: Communication Systems
166: Causality
167: To Label
170: Knowledge
185: System Accessibility
181: Structure
199: The Mission

200: Sanctuary
209: Enlist
210: Resolution
211: To Engage
212: Secure
215: Mobilize
219: Annihilation
220: Contemplation / Meditation
221: Either Way / Alignment
222: Cooperation
230: Resilience
250: To Thrive
255: To Emerge
266: Correlation

300: Crusade / Jihad
301: Confront
309: Consensus
310: Cell Net
311: Agreement
320: Deliberation
322: Oportunity
330: Win-Win Energy Management
333: Abundance
340: Abolitionism
355:
360: Technology
373: Remote Killing
370: Efficiency
390: Economicity

400: Earth Population
410: Permaculture
430: Ecosystem
440: Fellowship
444: Direct Digital Democracy

500: Assumption
501: Leadership
510: Admiration
511: Honorable
512: Altruism
520: Proficiency
530: Acceptance
535: Denoucing
540: Appreciation
550: Diplomacy
555: Gathering
556: To Pick Up Someone/Something
590: Excellency

600: Organizator
620: Diagnose
660: Operation
661: Operator
665: Role
666: Method
676: Deduce

700: Constitution
710: Intelligence
717: Desing
720: Quantum Mechanics
733: Argorithm Explaining
747: Artificial Intelligence
750: Consolidation
751: Enlightment
757: Prompt
766: Plan
770: The Gear
771: File
773: Algorithm Recoginzing
775: Output
777: Pattern / Rhetoric
778: Development
780: Systematization
799: Revolution Algorithm

800: Providence / Heroism
801: Production
802: Necessities
803: Resorces
804: Energy
808: Renewable Cycle
810: Permaculture
820: Management
830: Logistics
831: Scheme
832: Reach
833: Demand
834: Stock
835: Distribution
840: Consumption
850: Labor
860: Human Resources
863: Assignments
870: Structure
880: Peace
888: Globalization
890: Needs
899: Conception

900: Transparency
910: Institutions
911: Emergency Call
930: Energy Distribution
931: Only One Global Currency
960: Blockchain
962: Traceability
970: Optimination
990: Inspection
995: Accountancy
998: Regulation
999: Implementation
1000: Militancy
1001: Nova Era

1312: Boycott
1042: Drug Liberation
1100: Liberation Army
1400: Unity
1500: Benevolence
1550: Charity
1807: Black & Yellow
2222: Paradox
3000: Freedom
3100: Triumph
3330: We All Can Live In Abundance
4000: Coexist
5000: Glory
5500: Greatness
6999: Mystery
7220: Unified Field Theory
8000: Sustainability
8999: Finitude
9997: Discovery
9998: Unknown
9999: Universe
10000: Existence

. This is a numeric Matrix for communications purposes.
. This can be used to convey meaning.
Ex.: 6022: Good Reason to Resist.
. Mathematical operators can be used to calculate meaning.
Ex.: To liberate with a good force: 340. 300 + 40 = 340.
. Logical operators to create statements.
Ex.: ¬11: 13. If not Justice then Death.
. Colors can also be used as information.
- You can help build it.