What is BLAST Z?
Blastz is a nucleotide local alignment program developed by Webb Miller’s group at PSU (http://www.bx.psu.edu/miller_lab/). It takes FASTA or nib sequences as input and produces output in its own format, lav. Some notable algorithmic improvements over traditional blast: seeds matches using 12-of-19 tiles (see Ma et al.
What is a chain file genomics?
The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. Each set of chain alignments starts with a header line, contains one or more alignment data lines, and terminates with a blank line. The format is deliberately quite dense.
What is a Psi-BLAST?
Position-Specific Iterative (PSI)-BLAST is a protein sequence profile search method that builds off the alignments generated by a run of the BLASTp program. The first iteration of a PSI-BLAST search is identical to a run of BLASTp program (1).
How many genomes are available on BLAST?
This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes.
What is the difference between BLASTp and blastn?
The amino acid sequences being identical, blastp would have no problem in retrieving one sequence, using the other sequence as query. Blastn, however, uses a default word size of 11 nucleotides. This means the two sequences must match with at least 11 nucleotides for blastn to be able to report any hit at all.
What is the difference between blastn and BLASTx?
In summary, BLASTx searchs protein database using a translated nucleotide query whereas blastn for searching translated nucleotide database using a protein query.
What is a chain file?
A certificate chain is an ordered list of certificates, containing an SSL/TLS Certificate and Certificate Authority (CA) Certificates, that enable the receiver to verify that the sender and all CA’s are trustworthy.
What is a chain file liftOver?
A liftOver file is a chain file, where for each region in the genome the alignments of the best/longest syntenic regions are used to translate features from one version of a genome to another.
What is a Psi BLAST?
