bioutils

Routine utilities for seuqnece operation

align

Utilities for convert alignment file format and extract subsequences from an alignment.

• aln2nex.pl Convert alignment to NEXUS
• aln2phys.pl Convert alignment to sequential PHYLIP
• aln4phyml.pl Convert alignment to PHYLIP format for PhyML input (i.e., long seuqnec ID)
• alnscore.pl Score alignment
• comb_alns.pl Combine multiply algnment file into one
• extractalign.pl Extract regions of an alignment
• phy2paml.pl Convert PHYLIP alignment for PAML input.

blast2taxon

Parse NCBI BLAST report and store into an SQLite3 database. Also provided scripts to statistic BLAST reports in Excel format.

keggdb

Parse KEGG data and store into an SQLite3 database.

See also: Bio::KEGGI

seq

Utilities for routine sequence operation

• conv_date.pl Convert 'yyyy-mm-dd' format date in seuqnce id to day of year or decimal
• date2dec.pl Convert 'yyyy-mm-dd' format date to decimal
• dec2date.pl Convert decimal of year to date, in 'yyyy-mm-dd' format
• extractseq.pl Extract sequences from a multi-FASTA sequence file according to given sequence IDs
• gbk2embl.py Convert NCBI GenBank format file into EMBL
• get_seq_by_kw.pl Get seqences from a multi-FASTA file according to given keywords
• get_seqlen.pl Get sequence lenth
• grp_seq_by_len.pl Group sequences according to length
• rm_seq_by_id.pl Remove sequences according to given IDs
• rm_seq_by_kw.pl Remove sequences according to given keywords
• rnd_pick_seq.pl Random pick sequences from a multi-FASTA file
• seqlen.py Get sequence length
• sort_seq_by_len.pl Sort sequences according to sequence length
• split_seqfile.pl Split large multi-FASTA sequence file into many small files
• splitmf.pl same to above
• transeq.pl Translate nucleotide sequences into protein

sql_gui

A GTK2 interface to query SQLite3/PostgreSQL database.

taxonomy

Parse and load NCBI taxonomy into a local SQLite3 database.

Note: NCBI taxonomy in available at NCBI ftp

tree

Operation on phylogenetic trees.

• reduce_trees.pl Reduce the trees number of a BEAST analysis result.

virdb

Parse GenBank format viral genome file (usually downloaded from GenBank) and load into an SQLite3 database.

@2017-07-04: Added new scripts, fmt_gbf.py and upd_ga_info.py, to load GISAID sequences into the database. The work flow is:

1. Download nucleotide sequences from GISAID in FASTA formata. Keep the sequence header format is "DNA Accession no. | Isolate name | Type | Collection date".
2. Anntate GISAID nucleotide sequences by NCBI Influenza Virus Sequence Annotation Tool. Download the reports, in '.gbf' format.
3. Run script, fmt_gbf.py, to format the '.gbf' file into '.gbk' file.
4. Load re-formatted '.gbk' file into target database.
5. Load GISAID strain information (in a '.csv' file) into the database by script 'upd_ga_info.py'.