Tools for aligning sets of sequences to a reference sequence (for example, cDNA to genomic).
E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.
The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.
The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.
The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.
mRNA to Genome Alignments (MgAlignIt) aligns mRNA/EST to genome sequences and visualizes the alignment to provides intron/exon structure information.
Align cDNA with genomic DNA, allowing for introns and small number of sequencing errors.
The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.