Below are some useful links in bioinformatics and genomics.
Genomic databases
Integrated Microbial Database @ DOE Joint Genome Institute
http://img.jgi.doe.gov/cgi-bin/pub/main.cgi
GenBank @ National Center for Biotechnology Information
Regulatory databases
RegTransBase
Database of regulatory interactions on literature and expertly curated database of transcription factor binding sites
http://regtransbase.lbl.gov/cgi-bin/regtransbase?page=main
RegulonDB
Curated database of E. coli transcriptional regulation
PRODORIC
Prokaryotic database of gene regulation and systems biology
TRANSFAC
Knowledge base on transcription factors, their experimentally-proven binding sites and regulated genes
http://www.biobase-international.com/pages/index.php?id=transfac
TRED
Transcriptional Regulatory Element Database (Human, Mouse, Rat)
http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=home
DBSD
The Drosophila Binding Site Database
http://rulai.cshl.org/dbsd/index.html
Promoter databases
CEPDB
C. elegans Promoter Database
http://rulai.cshl.edu/cgi-bin/CEPDB/home.cgi
SCPD
The Promoter Database of Saccharomyces cerevisiae
CSHLmpd
Mammalian Promoter Database
http://rulai.cshl.edu/cshlmpd/
EPD
The Eukaryotic Promoter Database
https://epd.epfl.ch//index.php
PromEC
An updated database of E. coli mRNA promoters with experimentally identified transcriptional start sites
Online binding site search tools
MEME/MAST
https://meme-suite.org/meme/tools/meme
AlignACE
https://arep.med.harvard.edu/mrnadata/mrnasoft.html
BioProspector
http://ai.stanford.edu/~xsliu/BioProspector/
PhyloGibbs (Phylogenetic footprinting)
http://www.phylogibbs.unibas.ch/cgi-bin/phylogibbs.pl
Alignment software
Global
ClustalX
T-COFFEE
MUSCLE
MAFFT
https://mafft.cbrc.jp/alignment/server/
DIALIGN
http://bibiserv.techfak.uni-bielefeld.de/dialign/
Local
BLAST
http://blast.ncbi.nlm.nih.gov/Blast.cgi
FASTA
http://www.ebi.ac.uk/Tools/fasta33/index.html
LALIGN
http://www.ch.embnet.org/software/LALIGN_form.html
Alignment editors
JalView