jbrowse-plugin-msaview 2.8.2 → 2.9.0

package/src/LaunchMsaView/components/{NCBIBlastQuery/NCBIBlastPanel.tsx → BlastQuery/BlastPanel.tsx}

@@ -4,12 +4,14 @@ import SettingsIcon from '@mui/icons-material/Settings'
 import { IconButton } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 
-import NCBIBlastAutomaticPanel from './NCBIBlastAutomaticPanel'
-import NCBIBlastManualPanel from './NCBIBlastManualPanel'
-import NCBIBlastMethodSelector from './NCBIBlastMethodSelector'
-import NCBIBlastRIDPanel from './NCBIBlastRIDPanel'
-import NCBISettingsDialog from './NCBISettingsDialog'
-import { BASE_BLAST_URL } from './consts'
+import BlastAutomaticPanel from './BlastAutomaticPanel'
+import BlastManualPanel from './BlastManualPanel'
+import BlastMethodSelector from './BlastMethodSelector'
+import BlastSettingsDialog from './BlastSettingsDialog'
+import {
+  DEFAULT_EBI_EMAIL,
+  EBI_EMAIL_STORAGE_KEY,
+} from '../../../utils/ebiJobDispatcher'
 import { useLocalStorage } from '../../../utils/useLocalStorage'
 
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
@@ -21,14 +23,13 @@ const useStyles = makeStyles()({
 })
 
 const panelMap = {
-  automatic: NCBIBlastAutomaticPanel,
-  rid: NCBIBlastRIDPanel,
-  manual: NCBIBlastManualPanel,
+  automatic: BlastAutomaticPanel,
+  manual: BlastManualPanel,
 } as const
 
 export type BlastLookupMethod = keyof typeof panelMap
 
-export default function NCBIBlastPanel({
+export default function BlastPanel({
   handleClose,
   model,
   feature,
@@ -39,9 +40,9 @@ export default function NCBIBlastPanel({
 }) {
   const [lookupMethod, setLookupMethod] =
     useState<BlastLookupMethod>('automatic')
-  const [baseUrl, setBaseUrl] = useLocalStorage(
-    'msa-blastRootUrl',
-    BASE_BLAST_URL,
+  const [ebiEmail, setEbiEmail] = useLocalStorage(
+    EBI_EMAIL_STORAGE_KEY,
+    DEFAULT_EBI_EMAIL,
   )
   const [settingsOpen, setSettingsOpen] = useState(false)
   const { classes } = useStyles()
@@ -60,24 +61,19 @@ export default function NCBIBlastPanel({
         <SettingsIcon />
       </IconButton>
 
-      <Panel
-        model={model}
-        feature={feature}
-        handleClose={handleClose}
-        baseUrl={baseUrl}
-      >
-        <NCBIBlastMethodSelector
+      <Panel model={model} feature={feature} handleClose={handleClose}>
+        <BlastMethodSelector
           lookupMethod={lookupMethod}
           setLookupMethod={setLookupMethod}
         />
       </Panel>
 
       {settingsOpen ? (
-        <NCBISettingsDialog
-          baseUrl={baseUrl}
-          handleClose={newUrl => {
-            if (newUrl) {
-              setBaseUrl(newUrl)
+        <BlastSettingsDialog
+          ebiEmail={ebiEmail}
+          handleClose={settings => {
+            if (settings) {
+              setEbiEmail(settings.ebiEmail)
             }
             setSettingsOpen(false)
           }}

package/src/LaunchMsaView/components/{NCBIBlastQuery/NCBISettingsDialog.tsx → BlastQuery/BlastSettingsDialog.tsx}

@@ -6,27 +6,35 @@ import {
   DialogActions,
   DialogContent,
   DialogTitle,
+  Typography,
 } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 
-import { BASE_BLAST_URL } from './consts'
 import TextField2 from '../../../components/TextField2'
+import { DEFAULT_EBI_EMAIL } from '../../../utils/ebiJobDispatcher'
 
 const useStyles = makeStyles()({
-  urlField: {
+  field: {
     minWidth: 300,
   },
+  help: {
+    marginBottom: 8,
+  },
 })
 
-export default function NCBISettingsDialog({
+export interface BlastSettings {
+  ebiEmail: string
+}
+
+export default function BlastSettingsDialog({
   handleClose,
-  baseUrl,
+  ebiEmail,
 }: {
-  handleClose: (arg?: string) => void
-  baseUrl: string
+  handleClose: (arg?: BlastSettings) => void
+  ebiEmail: string
 }) {
   const { classes } = useStyles()
-  const [tempBaseUrl, setTempBaseUrl] = useState(baseUrl)
+  const [tempEbiEmail, setTempEbiEmail] = useState(ebiEmail)
   return (
     <Dialog
       open
@@ -37,22 +45,27 @@ export default function NCBISettingsDialog({
     >
       <DialogTitle>BLAST Settings</DialogTitle>
       <DialogContent>
+        <Typography variant="subtitle2" className={classes.help}>
+          Searches run at EBI, which asks for a contact address on every job so
+          they can reach whoever is generating the load. If your site sends real
+          volume, use your own.
+        </Typography>
         <TextField2
           autoFocus
           margin="dense"
-          label="BLAST Base URL"
+          label="EBI contact email"
           fullWidth
           variant="outlined"
-          value={tempBaseUrl}
-          className={classes.urlField}
+          value={tempEbiEmail}
+          className={classes.field}
           onChange={e => {
-            setTempBaseUrl(e.target.value)
+            setTempEbiEmail(e.target.value)
           }}
         />
         <Button
           variant="contained"
           onClick={() => {
-            setTempBaseUrl(BASE_BLAST_URL)
+            setTempEbiEmail(DEFAULT_EBI_EMAIL)
           }}
         >
           Reset
@@ -72,7 +85,7 @@ export default function NCBISettingsDialog({
           color="primary"
           variant="contained"
           onClick={() => {
-            handleClose(tempBaseUrl)
+            handleClose({ ebiEmail: tempEbiEmail })
           }}
         >
           Save

package/src/LaunchMsaView/components/{NCBIBlastQuery → BlastQuery}/CachedBlastResults.tsx

@@ -149,7 +149,7 @@ const CachedBlastResults = observer(function ({
               }}
             >
               <ListItemText
-                primary={`${getResultDisplayName(result)} - ${result.blastDatabase}/${result.blastProgram} (${result.msaAlgorithm})`}
+                primary={`${getResultDisplayName(result)} - ${result.blastDatabase}${result.blastProgram ? `/${result.blastProgram}` : ''} (${result.msaAlgorithm})`}
                 secondary={`${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...`}
               />
             </ListItemButton>

package/src/LaunchMsaView/components/BlastQuery/consts.ts

@@ -0,0 +1,22 @@
+/**
+ * Only used to build the link-out on the manual panel, which sends the user to
+ * NCBI's own site to run BLAST there. Nothing fetches this url: NCBI stopped
+ * sending Access-Control-Allow-Origin to third-party origins, so a browser
+ * cannot read a response from it at all. See docs/blast.md.
+ */
+export const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'
+
+export const msaAlgorithms = ['clustalo', 'muscle', 'kalign', 'mafft'] as const
+export type MsaAlgorithm = (typeof msaAlgorithms)[number]
+
+export const blastDatabaseOptions = [
+  'uniprotkb_swissprot',
+  'uniprotkb',
+  'uniprotkb_reference_proteomes',
+  'uniprotkb_trembl',
+] as const
+export type BlastDatabase = (typeof blastDatabaseOptions)[number]
+
+// curated, so it returns roughly one good sequence per species rather than the
+// many near-identical TrEMBL entries an alignment reads poorly
+export const defaultBlastDatabase: BlastDatabase = 'uniprotkb_swissprot'

package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx

@@ -4,8 +4,8 @@ import { Dialog } from '@jbrowse/core/ui'
 import { getSession } from '@jbrowse/core/util'
 import { Tab, Tabs } from '@mui/material'
 
+import BlastPanel from './BlastQuery/BlastPanel'
 import ManualMSALoader from './ManualMSALoader/ManualMSALoader'
-import NCBIBlastPanel from './NCBIBlastQuery/NCBIBlastPanel'
 import OrthologPanel from './OrthologQuery/OrthologPanel'
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel'
 import { readMsaDatasets } from './PreLoadedMSA/types'
@@ -41,7 +41,9 @@ export default function LaunchMsaViewDialog({
         }}
       >
         <Tab label="Orthologs (fast)" value="orthologs" />
-        <Tab label="NCBI BLAST query" value="ncbi_blast" />
+        {/* the tab value stays 'ncbi_blast' — it is only local state, and
+            renaming it buys nothing */}
+        <Tab label="BLAST query" value="ncbi_blast" />
         {hasPreloadedDatasets ? (
           <Tab label="Pre-loaded MSA datasets" value="preloaded_msa" />
         ) : null}
@@ -55,11 +57,7 @@ export default function LaunchMsaViewDialog({
         />
       </TabPanel>
       <TabPanel value={value} index="ncbi_blast">
-        <NCBIBlastPanel
-          handleClose={handleClose}
-          feature={feature}
-          model={model}
-        />
+        <BlastPanel handleClose={handleClose} feature={feature} model={model} />
       </TabPanel>
       {hasPreloadedDatasets ? (
         <TabPanel value={value} index="preloaded_msa">

package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx

@@ -13,13 +13,13 @@ import {
   getLinearGenomeView,
   getTranscriptDisplayName,
 } from '../../util'
+import MsaAlgorithmSelect from '../BlastQuery/MsaAlgorithmSelect'
 import LaunchPanelContent from '../LaunchPanelContent'
-import MsaAlgorithmSelect from '../NCBIBlastQuery/MsaAlgorithmSelect'
 import SubmitCancelActions from '../SubmitCancelActions'
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
 
-import type { MsaAlgorithm } from '../NCBIBlastQuery/consts'
+import type { MsaAlgorithm } from '../BlastQuery/consts'
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
 const useStyles = makeStyles()({

package/src/MsaViewPanel/components/JobLink.tsx

@@ -0,0 +1,17 @@
+import React from 'react'
+
+import { Typography } from '@mui/material'
+
+import ExternalLink from '../../components/ExternalLink'
+import { ebiBlastResultUrl } from '../../utils/ebiBlast'
+
+function JobLink({ jobId }: { jobId: string }) {
+  return (
+    <Typography>
+      Job {jobId} (
+      <ExternalLink href={ebiBlastResultUrl(jobId)}>see status</ExternalLink>)
+    </Typography>
+  )
+}
+
+export default JobLink

package/src/MsaViewPanel/components/LoadingBLAST.tsx

@@ -5,7 +5,7 @@ import { Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import RIDLink from './RIDLink'
+import JobLink from './JobLink'
 
 import type { JBrowsePluginMsaViewModel } from '../model'
 
@@ -18,57 +18,26 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
-function RIDError({
-  baseUrl,
-  rid,
-  error,
-}: {
-  baseUrl: string
-  rid?: string
-  error: unknown
-}) {
-  return (
-    <div>
-      {rid ? <RIDLink rid={rid} baseUrl={baseUrl} /> : null}
-      <ErrorMessage error={error} />
-    </div>
-  )
-}
-
-function RIDProgress({
-  baseUrl,
-  rid,
-  progress,
-}: {
-  baseUrl: string
-  rid: string
-  progress: string
-}) {
-  const { classes } = useStyles()
-  return (
-    <div className={classes.loading}>
-      {rid ? <RIDLink baseUrl={baseUrl} rid={rid} /> : null}
-      <Typography>{progress}</Typography>
-    </div>
-  )
-}
-
 const LoadingBLAST = observer(function LoadingBLAST2({
   model,
-  baseUrl,
 }: {
   model: JBrowsePluginMsaViewModel
-  baseUrl: string
 }) {
   const { progress, rid, error } = model
   const { classes } = useStyles()
   return (
     <div className={classes.margin}>
-      <LoadingEllipses message="Running NCBI BLAST" variant="h5" />
+      <LoadingEllipses message="Running EBI BLAST" variant="h5" />
       {error ? (
-        <RIDError baseUrl={baseUrl} rid={rid} error={error} />
+        <div>
+          {rid ? <JobLink jobId={rid} /> : null}
+          <ErrorMessage error={error} />
+        </div>
       ) : rid ? (
-        <RIDProgress baseUrl={baseUrl} rid={rid} progress={progress} />
+        <div className={classes.loading}>
+          <JobLink jobId={rid} />
+          <Typography>{progress}</Typography>
+        </div>
       ) : (
         <Typography>{progress || 'Initializing BLAST query'}</Typography>
       )}

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -27,7 +27,7 @@ const MsaViewPanel = observer(function MsaViewPanel2({
     <ErrorBoundary>
       <div>
         {blastParams ? (
-          <LoadingBLAST model={model} baseUrl={blastParams.baseUrl} />
+          <LoadingBLAST model={model} />
         ) : loadingStoredData ? (
           <div className={classes.loadingContainer}>
             <LoadingEllipses message="Loading MSA data" variant="h6" />

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -1,8 +1,8 @@
 import { makeId, strip } from '../LaunchMsaView/components/util'
 import { cleanProteinSequence } from '../LaunchMsaView/util'
 import { saveBlastResult } from '../utils/blastCache'
+import { queryEbiBlast } from '../utils/ebiBlast'
 import { launchMSA } from '../utils/msa'
-import { queryBlast, queryBlastFromRid } from '../utils/ncbiBlast'
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames'
 
 import type { JBrowsePluginMsaViewModel } from './model'
@@ -14,39 +14,24 @@ export async function doLaunchBlast({
 }: {
   self: JBrowsePluginMsaViewModel
 }) {
-  const {
-    baseUrl,
-    blastDatabase,
-    blastProgram,
-    msaAlgorithm,
-    proteinSequence,
-    selectedTranscript,
-    rid: existingRid,
-  } = self.blastParams!
+  const { blastDatabase, msaAlgorithm, proteinSequence, selectedTranscript } =
+    self.blastParams!
   const cleanedSeq = cleanProteinSequence(proteinSequence)
 
   const onProgress = (arg: string) => {
     self.setProgress(arg)
   }
 
-  if (existingRid) {
-    // publish it before the first poll so the view can link out to NCBI while
+  const { hits, rid } = await queryEbiBlast({
+    query: cleanedSeq,
+    blastDatabase,
+    onProgress,
+    // publish the job id before the first poll so the view can link out while
     // the job is still running
-    self.setRid(existingRid)
-  }
-
-  const { hits, rid } = existingRid
-    ? await queryBlastFromRid({ rid: existingRid, baseUrl, onProgress })
-    : await queryBlast({
-        query: cleanedSeq,
-        blastDatabase,
-        blastProgram,
-        baseUrl,
-        onProgress,
-        onRid: r => {
-          self.setRid(r)
-        },
-      })
+    onRid: r => {
+      self.setRid(r)
+    },
+  })
 
   self.setProgress('Fetching species taxonomy info...')
   const taxids = hits
@@ -81,7 +66,6 @@ export async function doLaunchBlast({
   await saveBlastResult({
     proteinSequence: cleanedSeq,
     blastDatabase,
-    blastProgram,
     msaAlgorithm,
     msa: result.msa,
     tree: result.tree,

package/src/MsaViewPanel/doLaunchOrthologs.test.ts

@@ -0,0 +1,159 @@
+import { beforeEach, describe, expect, test, vi } from 'vitest'
+
+import { doLaunchOrthologs } from './doLaunchOrthologs'
+import { launchMSA } from '../utils/msa'
+import {
+  COMMON_SPECIES,
+  fetchOrthologRows,
+  fetchProteinForGene,
+  resolveGeneId,
+} from '../utils/ncbiOrthologs'
+
+import type { JBrowsePluginMsaViewModel } from './model'
+import type { OrthologRow } from '../utils/ncbiOrthologs'
+
+// Every network call is mocked and nothing else is. What is under test is the
+// argument shaping either side of those calls -- which taxa get asked for, what
+// becomes the QUERY row, and whether the row earns the Accession that drives the
+// CDD overlay -- so the real COMMON_SPECIES list and the real
+// cleanProteinSequence stay in the picture.
+vi.mock('../utils/ncbiOrthologs', async importOriginal => ({
+  ...(await importOriginal<Record<string, unknown>>()),
+  resolveGeneId: vi.fn(),
+  fetchProteinForGene: vi.fn(),
+  fetchOrthologRows: vi.fn(),
+}))
+vi.mock('../utils/msa', () => ({ launchMSA: vi.fn() }))
+
+const mockResolveGeneId = vi.mocked(resolveGeneId)
+const mockFetchProtein = vi.mocked(fetchProteinForGene)
+const mockFetchRows = vi.mocked(fetchOrthologRows)
+const mockLaunchMSA = vi.mocked(launchMSA)
+
+const HUMAN = 9606
+const GENE_ID = '22861'
+const REPRESENTATIVE = { accession: 'NP_127497.1', sequence: 'MAGGAWGRLACY' }
+
+function makeModel(orthologParams: Record<string, unknown>) {
+  return {
+    orthologParams,
+    setProgress: () => {},
+  } as unknown as JBrowsePluginMsaViewModel
+}
+
+function params(extra: Record<string, unknown> = {}) {
+  return {
+    taxId: HUMAN,
+    geneCandidates: ['NLRP1'],
+    msaAlgorithm: 'clustalo',
+    ...extra,
+  }
+}
+
+// What fetchOrthologRows was asked for, which is the only place the taxa
+// default is observable.
+function taxaAskedFor() {
+  return [...mockFetchRows.mock.calls[0]![0].taxa].sort((a, b) => a - b)
+}
+
+// The QUERY row as it went to the aligner, read back out of the FASTA rather
+// than out of an intermediate, since the FASTA is what the alignment is of.
+function queryRowSent() {
+  return mockLaunchMSA.mock.calls[0]![0].sequence.split('\n')[1]
+}
+
+function queryMetadata(result: { treeMetadata: string }) {
+  return JSON.parse(result.treeMetadata).QUERY as Record<string, string>
+}
+
+beforeEach(() => {
+  vi.clearAllMocks()
+  mockResolveGeneId.mockResolvedValue({ geneId: GENE_ID, matched: 'NLRP1' })
+  mockFetchProtein.mockResolvedValue(REPRESENTATIVE)
+  mockFetchRows.mockResolvedValue([] as OrthologRow[])
+  mockLaunchMSA.mockResolvedValue({ msa: '', tree: '' })
+})
+
+describe('taxa', () => {
+  test('omitted asks for every species the dialog offers, less the query', async () => {
+    await doLaunchOrthologs({ self: makeModel(params()) })
+    expect(taxaAskedFor()).toEqual(
+      COMMON_SPECIES.map(s => s.taxId as number)
+        .filter(t => t !== HUMAN)
+        .sort((a, b) => a - b),
+    )
+  })
+
+  test('given is taken as written, less the query', async () => {
+    await doLaunchOrthologs({
+      self: makeModel(params({ taxa: [HUMAN, 10090, 9615] })),
+    })
+    expect(taxaAskedFor()).toEqual([9615, 10090])
+  })
+
+  test('an empty list is a request for no rows, not a request for all of them', async () => {
+    await doLaunchOrthologs({ self: makeModel(params({ taxa: [] })) })
+    expect(taxaAskedFor()).toEqual([])
+  })
+})
+
+describe('the QUERY row', () => {
+  test('omitted proteinSequence falls back to the representative protein', async () => {
+    await doLaunchOrthologs({ self: makeModel(params()) })
+    expect(queryRowSent()).toBe(REPRESENTATIVE.sequence)
+  })
+
+  test('a supplied sequence is used, and is cleaned first', async () => {
+    await doLaunchOrthologs({
+      self: makeModel(params({ proteinSequence: 'MAGG*AWGR&' })),
+    })
+    expect(queryRowSent()).toBe('MAGGAWGR')
+  })
+
+  test('throws when neither a sequence nor a representative is available', async () => {
+    mockFetchProtein.mockResolvedValue(undefined)
+    await expect(
+      doLaunchOrthologs({ self: makeModel(params()) }),
+    ).rejects.toThrow(/No query protein/)
+    expect(mockLaunchMSA).not.toHaveBeenCalled()
+  })
+
+  test('a failed representative lookup does not take down a launch that brought its own sequence', async () => {
+    vi.spyOn(console, 'warn').mockImplementation(() => {})
+    mockFetchProtein.mockRejectedValue(new Error('429'))
+    await doLaunchOrthologs({
+      self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
+    })
+    expect(queryRowSent()).toBe(REPRESENTATIVE.sequence)
+  })
+})
+
+// The Accession is what afterCreateAutoruns.autoLoadProteinDomains keys the CDD
+// overlay off, and attaching it to a row that is NOT the protein it names draws
+// every domain box at an offset. So the byte-identity guard is the assertion
+// here, in both directions.
+describe('the Accession that drives the domain overlay', () => {
+  test('is attached when the query row IS the representative protein', async () => {
+    const result = await doLaunchOrthologs({ self: makeModel(params()) })
+    expect(queryMetadata(result)).toMatchObject({
+      'Gene ID': GENE_ID,
+      Accession: REPRESENTATIVE.accession,
+    })
+  })
+
+  test('is withheld from a non-representative isoform', async () => {
+    const result = await doLaunchOrthologs({
+      self: makeModel(params({ proteinSequence: 'MDIFFERENTISOFORM' })),
+    })
+    expect(queryMetadata(result).Accession).toBeUndefined()
+  })
+
+  test('is withheld when the representative lookup failed', async () => {
+    vi.spyOn(console, 'warn').mockImplementation(() => {})
+    mockFetchProtein.mockRejectedValue(new Error('429'))
+    const result = await doLaunchOrthologs({
+      self: makeModel(params({ proteinSequence: REPRESENTATIVE.sequence })),
+    })
+    expect(queryMetadata(result).Accession).toBeUndefined()
+  })
+})

package/src/MsaViewPanel/model.ts

@@ -28,9 +28,8 @@ import {
 import type { MafRegion, MsaViewInitState } from './types'
 import type {
   BlastDatabase,
-  BlastProgram,
   MsaAlgorithm,
-} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
+} from '../LaunchMsaView/components/BlastQuery/consts'
 import type { Feature } from '@jbrowse/core/util'
 import type { Instance } from '@jbrowse/mobx-state-tree'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -46,13 +45,10 @@ export interface IRegion {
 }
 
 export interface BlastParams {
-  baseUrl: string
   blastDatabase: BlastDatabase
   msaAlgorithm: MsaAlgorithm
-  blastProgram: BlastProgram
   selectedTranscript?: Feature
   proteinSequence: string
-  rid?: string
 }
 
 export interface OrthologParams {

package/src/utils/blastCache.ts

@@ -2,9 +2,8 @@ import { createDbOpener } from './idb'
 
 import type {
   BlastDatabase,
-  BlastProgram,
   MsaAlgorithm,
-} from '../LaunchMsaView/components/NCBIBlastQuery/consts'
+} from '../LaunchMsaView/components/BlastQuery/consts'
 import type { DBSchema } from 'idb'
 
 const DB_NAME = 'jbrowse-msaview-blast-cache'
@@ -15,7 +14,12 @@ export interface CachedBlastResult {
   id: string
   proteinSequence: string
   blastDatabase: BlastDatabase
-  blastProgram: BlastProgram
+  /**
+   * Only ever set on rows cached by a version that still queried NCBI, where
+   * the choice between blastp and quick-blastp was real. Kept so those rows
+   * still display; never written now.
+   */
+  blastProgram?: string
   msaAlgorithm: MsaAlgorithm
   msa: string
   tree: string
@@ -51,7 +55,6 @@ const getDB = createDbOpener<BlastCacheDB>(
 function createCacheKey(
   proteinSequence: string,
   blastDatabase: BlastDatabase,
-  blastProgram: BlastProgram,
   msaAlgorithm: MsaAlgorithm,
   transcriptId?: string,
 ) {
@@ -59,13 +62,12 @@ function createCacheKey(
   // msaAlgorithm is part of the key because the stored msa/tree are produced by
   // it — without it, re-running the same query under a different algorithm
   // overwrites the earlier result and drops it from the history list
-  return `${blastDatabase}:${blastProgram}:${msaAlgorithm}${idPart}:${proteinSequence}`
+  return `${blastDatabase}:${msaAlgorithm}${idPart}:${proteinSequence}`
 }
 
 export async function saveBlastResult({
   proteinSequence,
   blastDatabase,
-  blastProgram,
   msaAlgorithm,
   msa,
   tree,
@@ -78,7 +80,6 @@ export async function saveBlastResult({
 }: {
   proteinSequence: string
   blastDatabase: BlastDatabase
-  blastProgram: BlastProgram
   msaAlgorithm: MsaAlgorithm
   msa: string
   tree: string
@@ -93,7 +94,6 @@ export async function saveBlastResult({
   const id = createCacheKey(
     proteinSequence,
     blastDatabase,
-    blastProgram,
     msaAlgorithm,
     transcriptId,
   )
@@ -101,7 +101,6 @@ export async function saveBlastResult({
     id,
     proteinSequence,
     blastDatabase,
-    blastProgram,
     msaAlgorithm,
     msa,
     tree,