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  1. Jalview
  2. JAL-1479

PDB<->Uniprot mappings from SIFTS

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    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Critical
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.10.0
    • Component/s: Structures
    • Labels:
      None

      Description

      Since circa Jalview 2.4, we rely on the needleman/wunsch to map between the alignment sequence and the displayed structures. This has two problems - it is not possible to view the extent of sequence with structure data, and the computed mapping may not always be the most accepted mapping for those data.

      PDBe provide an API to query SIFTS - this would allow mappings to be queried and shown as features on the sequence before structures are actually retrieved, and the most reliable mappings employed for mapping sequence data onto structure.

        Attachments

          Issue Links

          blocks

          New Feature - A new feature of the product, which has yet to be developed. JAL-1477 View all 'representative PDB structures' for selected sequences

          • Major - Major loss of function.
          • Closed
          depends on

          Task - A task that needs to be done. JAL-1942 Refactor DBRefFetcher

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1803 PDB chain id not saved in Jalview project

          • Critical - Crashes, loss of data, severe memory leak.
          • Closed
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-2356 SIFTS file cache is written but not read

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Resolved

          Bug - A problem which impairs or prevents the functions of the product. JAL-1827 incomplete sequence extracted from pdb entry 3a6s

          • Blocker - Blocks development and/or testing work, production could not run.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-1887 Incorrect start/end for sequence mapping in 'PDB - Sequence Mapping' window

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-1962 View mapping shows alignments between all chains when viewing multi-chain PDB

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-71 EBI uniprot record PDB database reference format changed

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Story - Created by Jira Software - do not edit or delete. Issue type for a user story. JAL-1963 SIFTS Complications

          • Major - Major loss of function.
          • Open

          New Feature - A new feature of the product, which has yet to be developed. JAL-1970 Add DBRefs via SIFTs

          • Major - Major loss of function.
          • Open

          New Feature - A new feature of the product, which has yet to be developed. JAL-1971 Add Secondary Structure Annotation from SIFTS

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Open

          New Feature - A new feature of the product, which has yet to be developed. JAL-1957 Provide multi-chain mapping for UniProt sequences using SIFTs

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-1999 Fail-safe mechanism for SIFTS mapping using a configurable PID threshold

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. JAL-1990 Add a progress indicator to Structure Chooser interface

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. JAL-3817 Add 'mapping method' to Structure Preferences help page

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1214 use pdb ID code in place of datafile when processing structure with Annotate3d service

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2007 Use PDBe numbering for sequences extracted from PDB files

          • Major - Major loss of function.
          • In Progress

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1281 Allow one to many associations for sequence and chains in a single PDB structure

          • Blocker - Blocks development and/or testing work, production could not run.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1711 allow PDB chain code to be specified when entering a specific PDB ID for a sequence

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1926 Add source information for Sequences at retrieval

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1967 Refactor mapping for sequence <-> (PDB resnum <-> PDB atom position)

          • Major - Major loss of function.
          • Closed

            Activity

              People

              Assignee:
              tcnofoegbu Tochukwu Charles N Ofoegbu
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: