NCBI Blast Home Page

Nucleotide sequence blast at the NCBI

BLAST stands for Basic Local Alignment Search Tool.The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your novel sequence. WU-BLAST 2.0 and NCBI BLAST2 are distinctly different software packages, although they have a common lineage for some portions of their code, so the two packages do their work differently and obtain different results and offer different features.

WU-BLAST2 stands for Washington University Basic Local Alignment Search Tool Version 2.0. The emphasis of this tool is to find regions of sequence similarity or homology quickly, with minimum loss of sensitivity.

Advanced WU-BLAST2 Search with post-processing at EMBL

TBLASTN search translated nucleotide database using a protein query.

Nucleotide Similarity Search. EBI services that provides sequence similarity search against nucleotide and protein databases using the FASTA programs. FASTA can be very specific when identifying long regions of low similarity especially for highly diverged sequences. Works also for full genomes. Software can be downloaded.

EBI service that provides sequence similarity searching against complete genomes databases using the FASTA programs.

At NCBI at NCBI

Compares a protein sequence or a protein profile HMM to a DNA sequence, allowing for introns and frameshifting errors. The software can also be downloaded.

Smith/Waterman type searches on Paracel's Fast Data Finder (FDF) at EMBnet-CH. The Smith-Waterman (S-W) search algorithm used by the FDF server is about 5% more sensitive towards divergent matches than the BLAST algorithm.

YASS is a similarity search tool of genomic (DNA/RNA) sequences in fasta or plain text format (it produces pairwise local alignments). This tool is currently developed and maintained by L. Noe and G. Kucherov of the LIFL Bioinfo / INRIA Futurs Sequoia group. Like most of heuristic DNA local alignment software (BLAST, FASTA, PATTERNHUNTER, BLASTZ ...) YASS uses seeds to detect potential similarity regions, and then tries to extend them to actual alignments. This genomic search tool enables to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seeds used in the search step.