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.

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

NucDiff provides information about the types of differences and their locations. It is possible to upload the results into genome browser for visualization and further inspection. It was written in Python and uses the NUCmer package from MUMmer[1] for sequence comparison.

Address of the bookmark: https://github.com/uio-cels/NucDiff

Metabuli is metagenomic classifier that jointly analyze both DNA and amino acid (AA) sequences. DNA-based classifiers can make specific classifications, exploiting point mutations to distinguish close taxa. AA-based classifiers have higher sensitivity in detecting homology between query and reference sequences, leverageing higher conservation of AA sequences. Metabuli combines the information of both sequence types using a novel k-mer structure, metamer, to enable both specific and sensitive characterization of metagenomic samples. In addition, it can classify reads against a database of any size as long as it fits in the hard disk.

Address of the bookmark: https://github.com/steineggerlab/Metabuli