DNA Analysis

DNA sequence retrieval and homology searches

Genbank
NCBI/Entrez (sequence retrieval/Genbank) 
NCBI BLAST (search for homology in sequence databases) 
EMBL
SRS (sequence retrieval system/EMBL) 
EMBL BLAST (search for homology in sequence databases) 
DDBJ
SRS (Sequence Retrieval System/DDBJ)

DNA sequence analysis

Online sequence alignment (www) and free software (s) 

ClustalW alignment www (global* sequence alignment, and treefile creation)
ClustalW, MSA, ctree www (three different alignment programs)
ToPLignwww (global, free shift* and local* alignments with multiple visualization modes)
Divide and Conquer (DCA) www global and free shift alignments
BLAST-2www (local alignment of two sequences)
ClustalW with JalView www (Jalview multiple sequence editor, has some neat analysis features)
BOXSHADEwww (preparing pre-aligned sequences for publication)
TreeViews (for viewing and editing treefiles, compliments of the University of Glasgow )
Webcutter - finds restriction sites in your sequence
Reverse complement (Harvard)- produces the reverse complement of your sequence

*Free shift alignments will ignore gaps at the beginning and end of the sequence, while Global alignments try to consider all positions.
Use Free shift alignments when some of the sequences are terminally truncated. Local alignments (such as BLAST) are useful for
finding short stretches of homology and are useful for finding sequence overlap or detecting a short internal sequence stretches that
are shared. 

PCR Primer Design

Primer 3 (lets you input target sequence and gives the best pair - very high rating)
Primer Design (good program)
PCR Primer Selection (a good primer modeling program)
Gene Fisher (another good primer modeling program)

Promoter Analysis

PLACE (search for known plant cis-acting elements)
PlantCARE (search for known plant cis-acting elements)
PROSCAN (detection of Eukaryotic promoter regions in genomic DNA)
Improbizer (novel motif detection using multiple sequences)
MEME (novel motif detection using multiple sequences)
MotifMatcher (find a known motif in a sequence)
MAST (search for a motif in a database, uses MEME output format)
Dnanalyze (TF mapping)
Dragon Promoter Finder 1.2 (TSS finder and promoter region analysis)
FunSiteP 2.1
HCtata (TATA signal prediction)
McPromoter Ver.3
MatInspector (Search for TF binding sites)
ModelGenerator and ModelInspector
NNPP2.1 (TSS finder)
PromoterInspector (Strand non-specific promoter region finder)
Promoter2.0 (TSS finder)
Promoter Scan II (Promoter region prediction)
RGSiteScan
Signal Scan (Search for Eukaryotic Transcriptional Elements)
TESS (Search for Transcription Elements)
TFSEARCH (Predicts TF binding sites based on TRANSFAC data)
TRANSFAC (TF database and a number of associated programs)
TSSG and TSSW

General

CMS molecular biology resource
Rockefeller Molecular Biology Toolkit