1. Top
  2. WebFPC
  3. SyMAP
  4. GBrowse
  5. Blast
  6. ReadSeq
  7. repeatMasker
  8. SSR
  9. Trace2Seq
WebFPC is a tool in the WebAGCol package developed by AGI. We use it to display fingerprint Contigs related to our work.

SyMAP (Synteny Mapping and Analysis Program), a software package for detecting and displaying syntenic relationships between sequenced chromosomes (pseudomolecules) and/or FPC physical maps. We localized it to display fingerprint Contigs related to our work.

GBrowse is a tool to display genome information. We use it to display fingerprint Contigs to reference genome sequence.
IRGSP Build 4.0
Blast (Regular BLAST, Blast2) stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990, 1997). It is a very fast search algorithm that is used separately for protein or DNA databases. and is best used for sequence searching, rather than for motif searching. We provides BLAST facility for the end sequence of clones in genome library we construct and the pseudo sequence of genome used as reference rice to which the physical map is align. To search other datasets and access further information on BLAST. please refer to

One major diffculty encountered in running sequence analysis software is the use of differing sequence formats by different programs. These formats differ in the presence of certain characters and words that indicate where different types of information and the sequence itself are to be found. ReadSeq is a extremely useful sequence formatting program can recognize DNA or protein sequence file in various formats ( IG|Stanford, GenBank|gb, NBRF, EMBL|em, GCG, DNAStrider, Pearson|Fasta|fa, Phylip3.2, Phylip|Phylip4, Plain|Raw, PIR|CODATA, MSF, PAUP|NEXUS, Pretty, XML, Clustal, FlatFeat|FFF, GFF, ACEDB, ) and writ a new file with an alternative format.

Repeat Mask
CENSOR is a software tool which screens query sequences against a reference collection of repeats and mask homologous portions with masking symbols, as well as generating a report classifying all found repeats.

SSR Search
Search simple sequence repeats in FASTA-formated DNA seqeucnes

Trace2Seq (Trace to sequence) is a pipeline can be used to process sequenceing data from ABI 3730 sequencher. After you submit the chrmatogram files, the pipeline will:
  • conduct base calling with phred;
  • trim low quality and vector sequence with lucy;
  • staistic some properties of sequence, such as length, base composition;

Then, at the output page, you can:
  • search sequence by project, submited date, and sequence motif;
  • download whole, or selected, sequence in batch model;
  • do blast against online database without download, copy and patse