Bio info

Matlab presentationArooba Baig

MATLAB   MATLAB is a high-level language and interactive

environment for numerical computation, visualization, and programming.

Features of Matlab you can analyze data, develop algorithms, Create models and applications.

Gene I selected

BCL2 B-cell CLL/lymphoma 2 [Homo sapiens (human)] Function

Transcriptional regulator that acts as an activator. Promotes beta-catenin transcriptional activity

Fasta format

>gi|568815580:c63319778-63123346 Homo sapiens chromosome 18, GRCh38 Primary AssemblyCTTCTCCCCACCCCTCGCCGCACCACACACAGCGCGGGCTTCTAGCGCTCGGCACCGGCGGGCCAGGCGCGTCCTGCCTTCATTTATCCAGCAGCTTTTCGGAAAATGCATTTGCTGTTCGGAGTTTAATCAGAAGAGGATTCCTGCCTCCGTCCCCGGCTCCTTCATCGTCCCCTCTCCCCTGTCTCTCTCCTGGGGAGGCGTGAAGCG

1-BASE LOOKUP

1-BASE LOOKUP Find nucleotide codes, integers, names, and complements

2-Dna to rna

converts a DNA sequence to an RNA sequence by converting any thymine nucleotides (T) in the DNA sequence to uracil nucleotides (U)

3- nt2int

Convert nucleotide sequence from letter to integer representation

4-seqcomplement

calculates the complementary strand of a DNA or RNA nucleotide sequence.

5-seqreverse

seqreverse calculates the reverse strand of a DNA or RNA nucleotide sequence

6-blosum

Return a BLOSUM matrix with the amino acids in a specific

order.

7-PAM

PAM returns the PAMN scoring matrix for amino acid sequences

8-Rna plot

draws the RNA secondary structure specified by RNA2ndStruct

9-JOINSEQ

Creat new sequence which is the combination of two seq 1 and seq 2

10-NWALING

nwalign (Seq1, Seq2) returns the optimal global alignment score in bits.

11-randseq

It creates a random sequence with a length specified by SeqLength

12-swalign

Swalign (Seq1, Seq2) returns the optimal local alignment score in bits. The scale factor used to calculate the score is provided by the scoring matrix.

13-amino lookup

Find amino acid codes, integers, abbreviations, names, and codons

14-basecount

base count(SeqNT) counts the number of each type of base in a SeqNT

15-Seqwordcount

Seqwordcount (Seq, Word) counts the number of times that a word appears in a sequence, and then returns the number of occurrences of that word.