https://prakharg24.github.io/papers/401851.full.pdf

Address of the bookmark: https://prakharg24.github.io/papers/401851.full.pdf

Transcription is the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: The Central Dogma of Molecular Biology: "DNA makes RNA makes protein" Here the process begins. Transcription factors assemble at a specific promoter region along the DNA. The length of DNA following the promoter is a gene and it contains the recipe for a protein. A mediator protein complex arrives carrying the enzyme RNA polymerase. It manoeuvres the RNA polymerase into place... inserting it with the help of other factors between the strands of the DNA double helix. The assembled collection of all these factors is referred to as the transcription initiation complex... and now it is ready to be activated. The initiation complex requires contact with activator proteins, which bind to specific sequences of DNA known as enhancer regions. These regions may be thousands of base pairs distant from the start of the gene. Contact between the activator proteins and the initiation-complex releases the copying mechanism. The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. Only one of the strands is copied. It acts as a template for the synthesis of an RNA molecule which is assembled one sub-unit at a time by matching the DNA letter code on the template strand. The sub-units can be seen here entering the enzyme through its intake hole and they are joined together to form the long messenger RNA chain snaking out of the top.

FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments:

• FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints.
• FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy.
• FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above.
• The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned (see the picture and movie at the top of the page).

You can see more information on the FAQ. 

Address of the bookmark: http://fsa.sourceforge.net/

https://salzberg-lab.org/

Address of the bookmark: https://github.com/pratas/smash

DNA:

Nucleotide Code: Base:

---------------- -----

A.................Adenine

C.................Cytosine

G.................Guanine

T (or U)..........Thymine (or Uracil)

R.................A or G

Y.................C or T

S.................G or C

W.................A or T

K.................G or T

M.................A or C

B.................C or G or T

D.................A or G or T

H.................A or C or T

V.................A or C or G

N.................any base . or -............gap

Protein:

Amino Acid Code: Three letter Code: Amino Acid:

---------------- ------------------ -----------

A.................Ala.................Alanine

B.................Asx.................Aspartic acid or Asparagine

C.................Cys.................Cysteine

D.................Asp.................Aspartic Acid

E.................Glu.................Glutamic Acid

F.................Phe.................Phenylalanine

G.................Gly.................Glycine

H.................His.................Histidine

I.................Ile.................Isoleucine

K.................Lys.................Lysine

L.................Leu.................Leucine

M.................Met.................Methionine

N.................Asn.................Asparagine

P.................Pro.................Proline

Q.................Gln.................Glutamine

R.................Arg.................Arginine

S.................Ser.................Serine

T.................Thr.................Threonine

V.................Val.................Valine

W.................Trp.................Tryptophan

X.................Xaa.................Any amino acid

Y.................Tyr.................Tyrosine

Z.................Glx.................Glutamine or Glutamic acid