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Start Search Launcher:
- Nucleic Acid Search
- General Protein Search
- Species Protein Search
- Multiple Sequence Alignment
- Pairwise Sequence Alignment
- Gene Features Searches
- Sequence Utilities
- Protein Structure Prediction
Other Services
- BCM Human Transcript Database
- BCM Gene Finder
- BCM Protein Structure Prediction
Choose a type of search from the pull-down menu
BCM Search Launcher: Nucleic Acid Sequence Searches
Cut and paste DNA sequence here (raw sequence only; no header, etc.);
Maximum sequence length is 7000 bases.
Sequence name/identifier (optional):
Choose search method / database:
[H]
[O]
[P]
[E]
=
[H]
:Help/description;
[O]
:full Options form;
[P]
:search Parameters;
[E]
:Example search
WU-BLASTX+BEAUTY /
nr protein
- Warren Gish's BLAST with gapped alignments,
RepeatMasker
, and BEAUTY post-processing (WU/BCM) [
H
] [
O
] [
P
] [
E
]
BLASTN /
nr dna
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
BLASTN /
BCM HTDB
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Unfinished htgs
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Finished htgs
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
BLASTN /
microbial genomes
- Gapped BLAST against both finished and unfinished microbial genomes (NCBI) [
H
] [
O
] [
P
] [
E
]
BLASTN /
dbest
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
TBLASTX /
dbest
- 6-frame translation vs. 6-frame dbest
TBLASTX with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
BLASTN /
month
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
BLASTN /
dbsts
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
BEAUTY-X / CRSeqAnnot
- Seq family and domain information added to BLASTX search of BCM CRSeqAnnot db (BCM) [
H
] [
O
] [
P
] [
E
]
tRNAscan-SE
- Search for tRNA genes in genomic sequence (BCM/WUSTL) [
H
] [
O
] [
P
] [
E
]
Rodent Specific Searches:
BLASTN /
est_mouse
- Gapped BLASTN with
RepeatMasker
, Entrez & SRS links (NCBI/UW/BCM) [
H
] [
O
] [
P
] [
E
]
Species Specific Searches:
BLASTN /
Actinobacillus actinomycetemcomitans
genome
- BLASTN 1.4 (OU) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Arabidopsis
Genebank
- Gapped NCBI BLAST2.0 with
RepeatMasker
(TAIR/UW) [
H
] [
O
] [
P
] [
E
]
BLASTN / Fungal
(Aspergillus nidulans and Neurospora crassa)
genomes
- BLASTN 1.4 (OU) [
H
] [
O
] [
P
] [
E
]
BLASTN /
B. subtilis
- BLAST2 search of B. subtilis strain 168 (Pasteur) [
H
] [
O
] [
P
] [
E
]
WU-BLASTN /
C. elegans
genomic
- 6-frame translation vs. genomic (Sanger) [
H
] [
O
] [
P
] [
E
]
WU-BLASTX /
C. elegans
wormpep
- 6-frame translation vs. wormpep (Sanger) [
H
] [
O
] [
P
] [
E
]
WU-TBLASTX /
C. elegans
EST
- 6-frame translation vs. translated
C. elegans
EST (Sanger) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Cryptococcus neoformans
genome
- BLASTN 1.4 (OU) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Drosophila
genome
- BLASTN 2.0 (NCBI) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Neisseria gonorrhoeae
genome
- BLASTN 1.4 (OU) [
H
] [
O
] [
P
] [
E
]
WU-BLASTN /
S.cerevisiae
Genome
- Warren Gish's BLAST with gapped
alignments (Stanford SGD) [
H
] [
O
] [
P
] [
E
]
WU-BLASTN /
S. pombe
genome
- Warren Gish's BLAST with gapped
alignments (Sanger) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Staphylococcus aureus
genome
- BLASTN 1.4 (OU) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Streptococcus pyogenes
genome
- BLASTN 1.4 (OU) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Streptococcus mutans
genome
- BLASTN 1.4 (OU) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Synechocystis sp. strain PCC 6803
Genome
- (CyanoBase) [
H
] [
O
] [
P
] [
E
]
WU-BLASTN /
ToxoDB
- WU-BLASTN search of the Toxoplasma database of clustered ESTs (UPENN) [
H
] [
O
] [
P
] [
E
]
BLASTN /
Trypanosoma brucei
genome
- BLASTN 1.4 search ofTrypanosoma brucei BAC and P1 End (TIGR) [
H
] [
O
] [
P
] [
E
]
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