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HMMER web server: 2015 update.

Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR - Nucleic Acids Res. (2015)

Bottom Line: Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture.The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user.Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK HHMI Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA rdf@ebi.ac.uk.

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Example of the expanded results table, showing the kingdom and species, number of significant hits, and the hit positions between the query and the target sequences after searching the UniProtKB sequence accession P00519 (amino acids 57 to 218) against the UniProtKB reference proteomes sequences (2014_10 release). The customise button in the top-right of the table header can be used to switch on different columns in that table (row count, secondary accessions, description, species, kingdom, known structure, number of identical sequences, number of hits, number of significant hits, bit score and graphical representation of the hit position). An expanded view of the hit position graphic is shown below the table. The enlarged view indicates where the two regions of similarity, or hits, in the query sequence match the target sequence. Each distinct hit of the query sequence is shown as a coloured box, and the corresponding aligned region is represented by a box of the same colour. The two sequences in each row are drawn proportionally to each other, with the sequence represented as a grey line. The two sequences are drawn left-justified (i.e. unaligned), with the query sequence always shown above the target. In this particular case, the order of the hits is reversed between the query and target sequences. A similar representation is used for queries with a profile HMM, with the top image (the query) representing the length of the profile HMM. The hit graphic quickly allows the identification of sequence rearrangements and repeated regions (where hit/coloured box in the query is duplicated multiple times in the target sequence).
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Figure 2: Example of the expanded results table, showing the kingdom and species, number of significant hits, and the hit positions between the query and the target sequences after searching the UniProtKB sequence accession P00519 (amino acids 57 to 218) against the UniProtKB reference proteomes sequences (2014_10 release). The customise button in the top-right of the table header can be used to switch on different columns in that table (row count, secondary accessions, description, species, kingdom, known structure, number of identical sequences, number of hits, number of significant hits, bit score and graphical representation of the hit position). An expanded view of the hit position graphic is shown below the table. The enlarged view indicates where the two regions of similarity, or hits, in the query sequence match the target sequence. Each distinct hit of the query sequence is shown as a coloured box, and the corresponding aligned region is represented by a box of the same colour. The two sequences in each row are drawn proportionally to each other, with the sequence represented as a grey line. The two sequences are drawn left-justified (i.e. unaligned), with the query sequence always shown above the target. In this particular case, the order of the hits is reversed between the query and target sequences. A similar representation is used for queries with a profile HMM, with the top image (the query) representing the length of the profile HMM. The hit graphic quickly allows the identification of sequence rearrangements and repeated regions (where hit/coloured box in the query is duplicated multiple times in the target sequence).

Mentions: The results table is now customisable to allow the user to include a range of additional data fields that provide information on the hit sequences and nature of the match. Figure 2 shows an example of the ‘Score’ results table, where these three additional columns (taxonomic classification of the organism to which each matched sequence belongs, number of significant hits, and a graphical display of the position of the hit(s) between the query and target) have been added using the ‘Customize’ button found in the header of the table. The highlighted example in Figure 2 illustrates the two hit regions between the query and target demonstrating that there has been a re-arrangement of the hit regions in the query sequence compared to the target sequence.


HMMER web server: 2015 update.

Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR - Nucleic Acids Res. (2015)

Example of the expanded results table, showing the kingdom and species, number of significant hits, and the hit positions between the query and the target sequences after searching the UniProtKB sequence accession P00519 (amino acids 57 to 218) against the UniProtKB reference proteomes sequences (2014_10 release). The customise button in the top-right of the table header can be used to switch on different columns in that table (row count, secondary accessions, description, species, kingdom, known structure, number of identical sequences, number of hits, number of significant hits, bit score and graphical representation of the hit position). An expanded view of the hit position graphic is shown below the table. The enlarged view indicates where the two regions of similarity, or hits, in the query sequence match the target sequence. Each distinct hit of the query sequence is shown as a coloured box, and the corresponding aligned region is represented by a box of the same colour. The two sequences in each row are drawn proportionally to each other, with the sequence represented as a grey line. The two sequences are drawn left-justified (i.e. unaligned), with the query sequence always shown above the target. In this particular case, the order of the hits is reversed between the query and target sequences. A similar representation is used for queries with a profile HMM, with the top image (the query) representing the length of the profile HMM. The hit graphic quickly allows the identification of sequence rearrangements and repeated regions (where hit/coloured box in the query is duplicated multiple times in the target sequence).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489315&req=5

Figure 2: Example of the expanded results table, showing the kingdom and species, number of significant hits, and the hit positions between the query and the target sequences after searching the UniProtKB sequence accession P00519 (amino acids 57 to 218) against the UniProtKB reference proteomes sequences (2014_10 release). The customise button in the top-right of the table header can be used to switch on different columns in that table (row count, secondary accessions, description, species, kingdom, known structure, number of identical sequences, number of hits, number of significant hits, bit score and graphical representation of the hit position). An expanded view of the hit position graphic is shown below the table. The enlarged view indicates where the two regions of similarity, or hits, in the query sequence match the target sequence. Each distinct hit of the query sequence is shown as a coloured box, and the corresponding aligned region is represented by a box of the same colour. The two sequences in each row are drawn proportionally to each other, with the sequence represented as a grey line. The two sequences are drawn left-justified (i.e. unaligned), with the query sequence always shown above the target. In this particular case, the order of the hits is reversed between the query and target sequences. A similar representation is used for queries with a profile HMM, with the top image (the query) representing the length of the profile HMM. The hit graphic quickly allows the identification of sequence rearrangements and repeated regions (where hit/coloured box in the query is duplicated multiple times in the target sequence).
Mentions: The results table is now customisable to allow the user to include a range of additional data fields that provide information on the hit sequences and nature of the match. Figure 2 shows an example of the ‘Score’ results table, where these three additional columns (taxonomic classification of the organism to which each matched sequence belongs, number of significant hits, and a graphical display of the position of the hit(s) between the query and target) have been added using the ‘Customize’ button found in the header of the table. The highlighted example in Figure 2 illustrates the two hit regions between the query and target demonstrating that there has been a re-arrangement of the hit regions in the query sequence compared to the target sequence.

Bottom Line: Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture.The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user.Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK HHMI Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA rdf@ebi.ac.uk.

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