Glossary

E-value

Expectation-value of a BLAST search

The E-value reported for each BLAST-hit represents the number of alternate alignments, with the same or better total score, that could be expected to occur in the database purely by chance. Thus, the lower the E-value, the more significant the match. The value depends upon the quality and length of the alignment, as well as the size of the database.

FASTA format

FASTA is a simple, ASCII based, text-file format for biological sequences. Minimally a FASTA file comprises a header line, initiated with the ">" character, followed by one or more lines containing nucleic acid or protein sequence in one-letter code. This is the most common input format for bioinformatics analysis programs and services.

Example

>gi|3402004|pdb|1MB1|  Mbp1 From Saccharomyces Cerevisiae
MSNQIYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHILKAANFAKAKRTRILEKEVLKETHEKVQGGF
GKYQGTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASPPPAPKHHHASKVDHHHHHH

(Detailed information)

HSP

High Scoring Pair

The fundamental unit of BLAST output. An HSP consists of an ungapped, local alignment result.

Example

>ref|NP_012165.1| Transcriptional repressor that binds to promoter sequences of 
the cyclin genes, CYS3, and SMF2; expression is induced by 
stress or starvation during mitosis, and late in meiosis; member 
of the Swi4p/Mbp1p family; potential Cdc28p substrate; 
Xbp1p [Saccharomyces cerevisiae]
Length=647

 Score = 50.7 bits (122),  Expect = 1e-06, Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 4/43 (9%)

Query  42   KVQGGFGKYQGTWVPLNIAKQLAEK
            +++GG+ K QGTW+P+ I++ L  +  F +   L P+F  DF 
Sbjct  347  RIRGGYIKIQGTWLPMEISRLLCLRFCFPIRYFLVPIFGPDFP  389

multi FASTA file

A sequence file that contains more than one FASTA formatted sequence. The sequences are simply concatenated. This is a common input format for multiple sequence alignment or motif-finding programs.

Example

>Homeobox associated Leucine Zipper from gi|3868845  (134..178)
KQTEVDCELLRKCCASLTEENRRLQMEVDQLRALSTTQLHFSDFV
>Homeobox associated Leucine Zipper from gi 21264431 (168..212)
KQTEVDCEFLKKCCETLADENIRLQKEIQELKTLKLTQPFYMHMP
>Homeobox associated Leucine Zipper from gi|6634483  (212.. 256)
KQTEVDCELLKRCCETLTDENRRLHRELQELRALKLATAAAAPHH

(Detailed information)