python: the longest palindromic substring (7)

python: the longest palindromic substring (7)

Abstract: Given a string, find the length of the longest palindromic substring.

Bioinformatics in Python: analyze SAM file

Abstract: SAM stands for sequence alignment determined by the aligner namely Bowtie.

Bioinformatics in Python: CpG islands

Abstract: hunt CpG islands in a genome sequence

Bioinformatics in Python: filter DNA sequence

Abstract: filter DNA sequences from the sequence from the GenBank format

Bioinformatics in Python: Download genome sequences from Ensembl

Abstract: The script is used for download the newest version genome annotations.

Bioinformatics in Python: Retrieve GO annotations

Abstract: retrieve GO annotations with a given specie from ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/

Bioinformatics in Python: retrieve GO terms

Abstract: Retrieve GO(Gene Ontology) terms from http://geneontology.org/, and save them into a dictionary

Bioinformatics in Python: retrieve sequence from NCBI

Abstract: retrieve genome sequence from the ftp site of NCBI, and save them into a fasta file in order

Bioinformatics in Python: calculate Kmer

Abstract: k-mer counting of a DNA sequence

Bioinformatics in Python: hunt motif

Abstract: implement regular expression to hunt motif sequences

Bioinformatics in Python: amino acid residues

Abstract: hunt amino acid residues and calculate its percentage

Bioinformatics in Python: read the file in gtf/gff3 format

Abstract: read gtf file and extract genome annotations


Bioinformatics in Python: Trim adapters

Abstract:Trim adapter’s sequence at the 3‘-end of reads

Bioinformatics in python: splice DNA

Abstract: get exons and introns

Bioinformatics in Python: enzyme digestion

Abstract: module the process of enzyme digestion

Bioinformatics in Python: GC content

Abstract: calculate GC content with a given DNA sequence

python: string (4) compress string

Abstract: compress string using numeric string or the zlib module for saving memory usage

bioinformatics in python: enzyme sites of genome sequences

Abstract: get all positions of a given enzyme sites

python-bioinformatics: read fastq file

Abstract : get coordinate, read sequences, and Q values from a fastq file using mycode  and biopython

python-bioinformatics: read fasta file

Abstract: read fasta file using mycode and biopython