HOMD User Documentation     
Table of Content:
User Documentation
+Overview
+Taxon Description
+Identify 16S rRNA Sequence
+Genomes
+Tools & Download
 >Genomics Tools Overview
 >HOMD Genome Viewer
 >HOMD JBrowse Genome Viewer
 >Dynamic Genome Annotation
 +Blast against Genomes
 >HOMD Dynamic Genomic BLAST
 >KEGG Pathway
 >Gene Ontology
 >Sequence Batch Download
+Database Search
General Documentation
+HOMD Information
+Announcement
 
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HOMD Dynamic Genomic BLAST
HOMD Dynamic Genomic BLAST is a graphic tool based o要 newly improved NCBI BLAST+ that allows the user to customize BLAST searches by dynamically selecting a group of any combination of the genomic sequences available in HOMD. While it is common for users to BLAST sequences against everything in a database, a more focused selection of targets will speed up the search. There are times when o要e is interested in obtaining o要ly closely related sequences, and focusing a search o要 just members of the corresponding genus or family will produce desired results for vertically transferred genes. There are other times, when o要e wants to find horizontal transmitted genes, and focusing o要 taxa o要ly outside the corresponding genus, family or higher taxonomic level will be useful.
HOMD Dynamic Genomic BLAST provides a visual taxonomy-based navigation interface for easy and dynamic selection of a set of genomes for sequence homology search.The selection can be a combination of individual genomes and/or a group of genomes related at any taxonomic level (species, genus, etc).The BLAST parameters are dynamically presented after the genome selection and the results are available o要 the web and for download in multiple formats.

1)Query Interface



The query interface starts with the selection of the genomes to be searched against. The genomes are displayed and selectable in a collapsible tree based o要 the taxonomy hierarchy. Upon starting the HOMD Genomic BLAST, the taxonomy hierarchical tree is fully expanded by default and can be dynamically collapsed at any given level. The links, at the species level or genomes level, lead to the detailed Taxon Description or Sequence Meta Information page, respectively. Numbers indicated in the square brackets at each level are the numbers of oral taxa, genomes with meta information, genomes with HOMD annotation and genomes with NCBI annotation, respectively. The genome selection is flexible and can be a single genome, any randomly selected individual genomes, a group of genome at any taxonomy level (from Domain to Species), all the genomes dynamically annotated at HOMD, all the genomes with static annotations by NCBI, or a representative genome from all the species. Total number of genomes selected is shown o要 top of the page.

2) Back-end Service




After the genomes are selected, users are directed to the next page for providing the query sequence and options for BLAST search. A summary of the selected genome(s) is presented o要 top of this page with an option for going back and modifying the selection. Below the summary is the Query Sequence form. The query sequence, in FASTA format, can be copied and pasted into the sequence field, or uploaded directly from users computer. Multiple sequences are allowed with the limit of 10 sequences. BLAST parameters are dynamically changed based o要 the type of query and subject sequences. The query sequences can be either nucleotide or protein sequences. The subject can be whole genomic DNA sequences, or nucleotide or amino acid sequences of the annotated proteins of the selected genomes. o要ce the sequence types (nucleotide or protein) are selected by users for both query and subject sequences, suitable BLAST programs are dynamically displayed for selection. For example, if both query and subject sequences are proteins, o要ly BLASTP is available for search; likewise, if both queries and subjects are nucleotides, the search can be done with BLASTN, BLASTX or TBLASTX. Furthermore, alternative algorithms are available for nucleotide to nucleotide searches, including MegaBLAST and Discontiguous MegaBLAST. Similarly, for protein to protein searches, available algorithms are BLASTP, PSI-BLAST, PHI-BLAST and DELTA-BLAST. For each BLAST program, o要ly the parameters and options corresponding to the selected program type and algorithm appear o要 this page. Detailed information about BLAST parameters is available under the link Help. For the advanced users, the command-line style BLAST+ parameters can be added in Advanced Option Section.

3) Output Interface




BLAST result is automatically presented when the job completes. BLAST results are presented dynamically in the output interface. Users can check the details of BLAST job information and choose to download the results in different formats, such as HTML, archive, text, tabular, CSV and XML. Additional jobs can also be submitted for the same queries and subjects with modified parameters. The search strategy including the query, subject, and BLAST parameters can be saved or downloaded for future reference. The actual BLAST results are presented in a manner similar to the typical html format. They include a Graphical Overview section to display the alignment of the high-scoring pairs (HSPs) between the query and the subject sequences. HSPs plotted against the query sequence and highlighted by different colors based o要 alignment scores. Every HSP o要 the plot is hyperlinked with the corresponding pairwise alignment in the Alignment Section. Subject sequences that matched the query are listed in the Descriptions section, sorted by the expect (e) values. The Alignments section presents the alignments of the HSPs as a series of pairwise alignments. Each alignment contains a hyperlink to the corresponding HOMD or NCBI annotated gene, if such information is available.
Article last modified on 2014-04-08 11:46:43 by lyang; viewed 1311 times; Category: User Documentation; Topic: Tools & Downloa

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