Bioinformatics part 3 Sequence alignment introduction

This Bioinformatics lecture explains the details about the sequence alignment. The mechanism and protocols of sequence alignment is explained in this video lecture on Bioinformatics.
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In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.[1] Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Sequence alignments are also used for non-biological sequences, such as those present in natural language or in financial data.
Very short or very similar sequences can be aligned by hand. However, most interesting problems require the alignment of lengthy, highly variable or extremely numerous sequences that cannot be aligned solely by human effort. Instead, human knowledge is applied in constructing algorithms to produce high-quality sequence alignments, and occasionally in adjusting the final results to reflect patterns that are difficult to represent algorithmically (especially in the case of nucleotide sequences). Computational approaches to sequence alignment generally fall into two categories: global alignments and local alignments. Calculating a global alignment is a form of global optimization that "forces" the alignment to span the entire length of all query sequences. By contrast, local alignments identify regions of similarity within long sequences that are often widely divergent overall. Local alignments are often preferable, but can be more difficult to calculate because of the additional challenge of identifying the regions of similarity. A variety of computational algorithms have been applied to the sequence alignment problem. These include slow but formally correct methods like dynamic programming. These also include efficient, heuristic algorithms or probabilistic methods designed for large-scale database search, that do not guarantee to find best matches.
Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. (This does not mean global alignments cannot end in gaps.) A general global alignment technique is the Needleman--Wunsch algorithm, which is based on dynamic programming. Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith--Waterman algorithm is a general local alignment method also based on dynamic programming.
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[@melaniea.334]

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[@HarshSingh-qr5lm]

Wow! He explained the basics in such a simple way. Thank you, I got my doubts cleared in just first watch.

[@chakirahamada5689]

Thank you very much. I always try to understand this from books but I was everytime confused by the expressions " match" , "missmatch" .. in this context. Now It's clear thank you.

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[@293nevena]

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[@shomusbiologyofficial]

Glad to hear that you're getting benefit from my lectures

[@ElectroPineapple]

Kudos and thanks for such in-depth and easy to understand lectures on Sequence Alignment. Really like how you explain everything both visually and using examples.
Cheers from Pakistan!

[@TheSha2404]

I wish you teach my bioinformatics class... Thank you for clearing everything up! (y)

[@febaeldhose673]

I'm a zoology student but I'm interested to gain bioinformatics knowledge.your classes have encouraged me to continue in this field of study. Thankyou so much

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[@airisgraham2660]

Thanks for breaking this down so that us beginners can understand better!

[@titoman319]

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[@mattralston4969]

Thank you Shomu. Nice introductory lesson, was easy to follow

[@brightonsallvin8568]

Thank you for ur wonderful presentation sir ...it really awesome to know the basic of aligment information ..

[@DcayD]

You explained it better than any book... thanks

[@sumaiyasharmin3893]

You're an awesome teacher. Thank you and keep up the good work

[@scaryromangamingplatform4872]

Watching your all videos in 2021 ❤️
You were amazing before years you r amazing today also 😎❤️😍

[@Unique_universe91]

This really help me to understand sequence allignment..
Thank u sir 😊

[@thecompletelifestyle]

finally i understood the concept ot alignment and grading. thank youuuu :)

[@tarzengamingsquad464]

May God bless us with such dedication that you have. 🥺✨

[@tarzengamingsquad464]

Ameen

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Thank you

[@evertonsilvamota2509]

Another amazing video!!!! congratulations!!!! and thank you!

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[@uzmashaikh1007]

Your explanation is very simple. It is really easy to understand.

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[@mayukhroy5393]

Thank You Sir, this video was very helpful.

[@ibrahimssali7360]

Thanks for simplifying what we thought was complex

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[@titoman319]

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[@abhishekmajumdar6523]

Highly appreciated lecture series 👍

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Thank you

[@scaryromangamingplatform4872]

Thankyou For these videos...Helped Me to cover My 80% syllabus of bioinformatics.

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I am glad

[@mufongg]

Which textbook do you prefer for basic bioinformatics lesson?

[@christaljaneapuya3278]

Thank you sir! You're helping me a lot about this topic😊

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You're welcome. Glad to hear that you're getting benefit from my lectures

[@thatrandomgirl9234]

really helped me ! THANKYOU :)

[@wanderingrogue3039]

Would be really awesome if you collab with a computer scientist to make videos that analyse common algorithms in bioinformatics.

[@mattgraves3709]

Wow, this is an excellent series.
Where did you study if you don't mind me asking Shomu?

[@delpinsudha640]

Thank you sir. Your lecture was so good

[@shomusbiologyofficial]

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[@adeshinaodugbemi8412]

You made it so simple. You are a great teacher. Thank you!

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[@reardelt]

The goal is to maximise the score and not the number of matches as you said. An alignment can have a higher score than another even if it has a lower number of "matches".

[@AnujGuruacharya]

he does talk about "marks" as a way of grading the alignment... "mark" is a another word for "score"... so he does talk about maximizing the "marks" of the alignment in the middle of the video...

[@suzannecoveley6545]

Your hair looks great in this video

[@IshikaSharma]

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[@shomusbiologyofficial]

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[@onezaalvi9866]

i really appreciate your hardwork . its so helpful reallyyy

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[@user-ml1kg1wb4s]

great lecture, THX!

[@rituraj125]

It is really very helpful sir...Thank you so much for your efforts.

[@shomusbiologyofficial]

You're welcome

[@ccboo6811]

Hi. I'm having a hard time finding a source of information and understanding what I need to report for our bioinformatics class. Can you help me about introduction to Multiple Sequence Alignment? Is this just similar to Multiple? Would appreciate the help. Thanks

[@qingli9497]

Thanks so much!! I have several questions--why mismatch get higher score than gap? how these scores determined?and is the computer using these three(-2, -1,+2) scores to align the sequences? thank you !!

[@guilhermefial1686]

If a gap would have a higher score than a mismatch, then when aligning mismatching parts of the sequence, the algorithm would just introduce gaps until matching amino acids would be found, leading to a full of gaps alignment which is most likely wrong since gaps are more rare than replacements.

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[@ar.sayeem]

watching in 2022(11.02.22), I have to say , it is a great video , thank you brother

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[@shwetagupta9004]

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[@DiscoverTips]

very impressive tutorial

[@muralithatholu2113]

Simply superb.thank you sir

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[@ranjeethabm7002]

Thank you so much sir 😊😊

[@ritikakhanna7451]

Thankyou Sir... Very very informative videos.

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[@tabykhan5734]

hi, love the videos, but can you post the link to part 1 and 2 please!

[@aelitastones8012]

I love this!

[@aditijoshi4959]

My all time Go To RUclips Channel. Thank you sir :))

[@shomusbiologyofficial]

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[@cheonjej766]

How do know values of match, mismatch & gap ?

[@swatijain6343]

Thank you so much sir it is a very easy way to understand

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[@mtamamhariri2067]

I am from Indonesia. Thanks for your video.

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[@punitsalimath225]

I have a question, why was Alanine from S1 not aligned with Alanine from S2? that would yield higher score. If you changed TCG, why not A?

[@tinkerer371]

that was a really nice lesson,but lemme ask u dis u r considering a bottom up approach here,now is it possible to attempt a top-down approach,or is it just convention.
if it had been possible at all then will there exist some sort of equivalence between the two?Please reply anybody..

[@soumyashah6982]

which multiple sequences alignment method used for inconsistent order of nodes?

[@farzanayasmin6173]

Thanks for your great lecture from Bangladesh

[@shomusbiologyofficial]

Glad to hear that you're getting benefit from my lectures

[@knaupy]

thank you so much !

[@hkj7044]

Sir I done my twelfth with non-medical and graduation with physical science, is i am eligible for masters in bioinformatics?

[@discriplinehelpusDas]

Great explanation

[@shomusbiologyofficial]

Thank you

[@passionareeramshaikh9396]

Superbbbbbb explaination sirr

[@shomusbiologyofficial]

You're welcome

[@shailasingla8549]

Hi sir
Your lectures are so informative and helpful.
I want to ask that the score for the match mis match and gap are fixed or we can give it as per our wish.

[@Mohansir.onlinetech.academy]

sir I would like to thnx for this video, I have one question if we have same type of protein sequences from different species or different protein sequences of same species then what we will choose local or global alignment?

[@newnavee]

thank you sir

[@zapy422]

Hi all
Are there videos for alignment practices?
Thanks

[@WaseemAkram-ov7ye]

U are really helpful

[@shomusbiologyofficial]

Thank you

[@juliasouzaEV]

I feel the obligation of liking and comenting your videos.

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Thank you

[@saroshkhan6259]

Sir you are always helpful 😇😇😇😇😇😇

[@shomusbiologyofficial]

You're welcome. Glad to hear that you're getting benefit from my lectures

[@avsteluguvlogs1374]

mama nuvvu thoppu !

[@ahmadbakar6013]

sorry, in multiple alignment , query sequence are more than one? or one query sequence will be aligned with more than one sequences ?

[@NurulHikmawati]

My question is what's the best alignment method? Global or kocak?

[@md.hossenrony1985]

i just want to know that in ur 2nd sequence there are only 3 bases
is it possible to make a DNA sequence with 3 bases
if not then sir why u use that sort of sequence
if yes i have no complain
can anyone explain this
thanks in advanve

[@MohamedSiddig]

Very informative and clear explanations

[@shomusbiologyofficial]

Thank you. Glad you liked my lectures

[@raivandana2251]

May i ask one thing i am New in this bioinformatics course
Initially in this video u said some
Chou method i didn't get that part in previous part.. where does it belongs

[@sarakazmi6595]

Superb explanation

[@shomusbiologyofficial]

You're welcome

[@rishita_sharma4805]

Sir i understood very well thanks❤ but the second example you gave i can only make two cases one gives a result of -4 and other -1 is that right

[@shambhavisidhant2330]

really nice

[@kishanikandasamy]

Awesome bro

[@shomusbiologyofficial]

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[@yeasminara4418]

Want to know about dot plot

[@rajusrkr5444]

hello sir , could u plz suggest me one research topic in bioinformatic with data mining concepts for phd ?

[@hebahalfrajeen850]

can you tell me please the goal of alignment ? I understood the meaning but what the benefit of it ?

[@Mirror_2]

Part 3 content is different and not in sequence with previous contents of what we have studied in part 1 and 2 ??

[@imamuddinazmi2621]

Thank You So Much Sir 👍🏻😊

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[@shaanabello6663]

Thank you this was very helpful

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[@gayatriasawa2721]

Sir, I have not understood that what will be ans of seq S1 and S2 i.e alignment A1 which will align with S3.....I mean A1 will be number or it will be in the form of ATGC n so on
Plz explain

[@gayathrisenanayake4988]

yes it was helpful thank you !

[@shomusbiologyofficial]

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[@justvibing8379]

Thank you sir 😇

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[@tugbasehitogullar9457]

For the given seed list XX=..,XK=XK, KK=KK, KS=… which one is the most conserved amino acid ? How can I solve this problem , please help :)

[@dr.md.ismailhossain2681]

very good lecture

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[@abhinavdayal9512]

nice work sir

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Thank you

[@numankhan4319]

Vvvvvvvrey good class....
Love from pakistan...

[@shomusbiologyofficial]

Thank you so much for appreciating my efforts

[@kavitamojawat1861]

Plzz upload video on sequence alignment methods

[@JuliusUnique]

how can a gap be in a sequence? because of bad measurements or is it just normal that biological sequences have gaps?
and why is a gap worse than a mismatch?

[@gemechubekele2546]

Basically, these sequence alignments are to find out evolutionary relationships between sequences and that means possible mutations that happened on parent sequence. As such, gaps are representative of insertions and deletions(indels). Mismatch represent possible substitution mutations.

[@dr.sanjaysrivastva3372]

Very informative

[@shomusbiologyofficial]

Thank you

[@zebriahpatiencezhuwao9002]

Thanks sir!

[@shomusbiologyofficial]

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[@mmuzammil9188]

.....assigning scores, like for match is 2, for mismatch is -1 and for gap is -2 is it just for getting concept or actual? I mean does software score alignment the same values or values for scoring may be different?

[@goharfayazkhan]

It is just for giving you concept.

[@doctorofpharmacologytoxico9556]

Thank you.

[@shomusbiologyofficial]

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