Perl: Download genome annotations from NCBI FTP site

Abstract: Download genome sequences including DNA, RNA and protein sequences as FASTA or annotation in GFF format.

Perl: Achieve annotations based on accession number

Abstract: Here I showed how to achieve annotations of genes or proteins from GenBank, EntrezGene, and SwissProt.

Perl: make sequencing alignment using local blast

Abstract: Carry out sequence alignment and extract the results using the aligner blast2+ at the local computer

Perl: Storage of huge hash (2)

Abstract: Load huge nested hash into disk using the DBM::Deep module.

Perl: Storage of huge hash (1)

Abstract: Disk storage of huge hash will save RAM memory and speed up searching of hash.

Perl: Download file from URL

Abstract: implement the Perl package LWP::Simple to download files.

Perl: Equivalent codes instead of BioPerl (1)

Abstract: Here are the two equivalent codes for extract sequences from a FASTA file. One implement Bio::SeqIO, and the other implement only standard Perl codes.

Perl: Hash operations

Abstract: introduce some useful hash data structures.

Perl: Retrieve sequences

Abstract: Retrieve DNA/protein sequence and their annotations from the databases:GenBank, Swissprot, and EntrezGene.

Perl: Split string

Abstract: Split string using different patterns.

Perl: Preparation of FASTA and GTF files for RNA-seq

Abstract: The FASTA and GTF/GFF format files should be prepared when genome mapping using the aligner.

Perl: Use R commands in Perl

Abstract: How to use R commands in Perl script using the Perl package Statistics::R.

Perl: Genome annotations from GBK format file

Abstract: Convert GBK format file into FASTA format file based on the annotated features in GBK files.

Parallel computing using multi-threads

Abstract: Multi-threading programming can speed up analytic work.

Perl: Skills for reading text files in Perl

Abstract: How to open a file handle to access text contents.

Perl: DNA sequence manipulation

Abstract: Truncation, reverse-complementary, translation of DNA sequence.

Perl: Extract sequences from FASTA format files

Abstract: extract sequences from FASTA format file using the Bio-perl module.

Perl: Ordering in Perl

Abstract: How get a data set by order using array and hash.