bio info
TRANSCRIPT
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Matlab presentationArooba Baig
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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.
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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
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1-BASE LOOKUP
1-BASE LOOKUP Find nucleotide codes, integers, names, and complements
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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)
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3- nt2int
Convert nucleotide sequence from letter to integer representation
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4-seqcomplement
calculates the complementary strand of a DNA or RNA nucleotide sequence.
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5-seqreverse
seqreverse calculates the reverse strand of a DNA or RNA nucleotide sequence
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6-blosum
Return a BLOSUM matrix with the amino acids in a specific
order.
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7-PAM
PAM returns the PAMN scoring matrix for amino acid sequences
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8-Rna plot
draws the RNA secondary structure specified by RNA2ndStruct
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9-JOINSEQ
Creat new sequence which is the combination of two seq 1 and seq 2
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10-NWALING
nwalign (Seq1, Seq2) returns the optimal global alignment score in bits.
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11-randseq
It creates a random sequence with a length specified by SeqLength
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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.
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13-amino lookup
Find amino acid codes, integers, abbreviations, names, and codons
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14-basecount
base count(SeqNT) counts the number of each type of base in a SeqNT
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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.
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