Blast

Databases:

LTRs: To compare nucleotide queries with a LTR sequence database.
Genome: To compare both nucleotide and protein queries with a database of LTR retroelement genomes.
Cores: To compare both nucleotide and protein queries with a database of protein domains.

Search programs:

BLASTP: Identify a protein query or find protein sequences similar to the query.
BLASTX: Find similar proteins to translated DNA queries in a protein database.
BLASTN: Identify a DNA query or find DNA sequences similar to the query.
TBLASTN: Find similar sequences to a protein query in a nucleotide database.

Query:

Enter a single sequence in FASTA format:

Upload a multiple sequence file in FASTA format:

NOTE: When uploading a multiple sequence file, this window can be closed after submission as you will receive a mail
notification containing a link to the output result file.

Select multiple sequence FASTA file:

Limit output to n best hits:

E-mail address for notifications:


Select database and search:

Database:
Search program:

Options:

Expect:    Matrix:
Limit output to n best alignments:
Search domain:


NCBI-BLAST references:

  • Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. 1997. "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
  • Availability: http://www.ncbi.nlm.nih.gov/Tools



Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.
Cite this project:

Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061

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