EST Projects at YMU

Glossary

aa-fly:

  BDGP Translated polypeptide (Release 2)

Base-calling :

  We use phred to extract sequence from trace file. Only those sequences whose quality values are greater than 20 will be saved.

Decontamination :

  We use EST search against E.coli db , Lambda db,  Mitochondria db, rRNA db and vector db by using Blast . If the blast results with identity > 0.95 and E-value = 0, then we define the sequence contaminated and will remove it

EST-all :

  est_human (Non-redundant Database of Human GenBank+EMBL+DDBJ EST sequences)+ est_mouse (Non-redundant Database of Mouse GenBank+EMBL+DDBJ EST sequences)+ est_others(Non-redundant Database of all other organisms GenBank+EMBL+DDBJ EST sequences)

EST-other:

  est_others(Non-redundant Database of all other organisms GenBank+EMBL+DDBJ EST sequences)

Identity % :

  identity  length / aligned length

NR :

  All non-redundant GenBank CDS translations + PDB  +  SwissProt + PIR

Rice_pep :

  Oryza sativa protein db from TIGR

SP6 and T7 :

  sequence primers

Short seq :

  Sequences whose lengths are shorter than 100 bp

Unigene :

  Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.

Uni_At:

  UniGene Build Arabidopsis thaliana

Uni_Os:

  UniGene Build Oryza sativa

Vectorstrip :

  We use EMBOSS : vectorstrip to trim vector sequence