Difference between revisions of "Biopython/C2/Blast/Khasi"

| Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka ''' BLAST''' da kaba pyndonkam ki tools u '''Biopython'''

| Ha kane ka tutorial, ngin pule ban: '''run''' "BLAST" na ka bynta ka '''query sequence''' da kaba pyndonkam ki tools u Biopython.

| Bad, '''parse''' ia u BLAST output ban wad bniah shuh shuh.

|Ban bud ia kane ka tutorial, phi dei ban tip bha iaka undergraduate Biochemistry lane Bioinformatics.

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| Peit ia ka '''Python''' tutorials na ka link ba ai harum.

| Ban record ia kane ka tutorial, nga pyndonkam da ka: * '''Ubuntu''' Operating System version 14.10   

| '''BLAST''' ka dei ka ktien lyngkot jong ka '''Basic Local Alignment Search Tool.'''

| Ka dei ka '''algorithm''' ban ia nujor ki '''sequence''' information.

| Kane ka program ka ia nujor ia ki '''nucleotide''' lane '''protein''' sequences sha ki sequences ha ki databases bad khein ia ka statistical significance jong ki jingiahap.

| Ka Local '''BLAST''' ha ka machine jong phi lane run '''BLAST''' lyngba ka Internet lyngba ka NCBI servers.

| Ki don ar tylli ki rukom ban run ia ka '''BLAST''' ha ka '''Biopython'''     

| Nyngkong, run ia ka '''BLAST''' na ka bynta ka '''query sequence''' jong phi bad pynioh katto katne ka output.  

| Ba ar, '''parse''' ka '''BLAST''' output na ka bynta ka jingwad ba kham bniah hadien.  

| Ngin plie ia ka '''terminal''' bad run '''BLAST''' na ka bynta ka nucleotide sequence.  

| Plie ia ka terminal da kaba nion lang ia '''Ctrl, Alt''' bad '''T''' keys.

| Ha ka '''prompt''', type: '''ipython''' bad nion '''Enter'''.

| Ha kane ka tutorial, ngan sa pyni kumno ban run ia ka '''BLAST''' lyngba ka internet da kaba pyndonkam ka '''NCBI BLAST''' service.

| Type kumne harum ha ka prompt: '''from Bio.Blast Import NCBIWWW''' Nion '''Enter'''.

| Ka ba bud, ban '''run''' ia u BLAST lyngba ka internet, type ia kaba harum ha ka prompt.result= NCBIWWW.qblast"blastn","nt","186429").

| Ngin pyndonkam da ka '''qblast function ''' ha ka '''NCBIWWW '''module.

| '''qblast function''' ka shim lai tylli ki '''arguments''':

| Ka '''argument''' ba nyngkong  ka dei ka '''blast program''' ba pyndonkam naka bynta ban wad.

| Ba ar, pyntikna ia ka databases ban wad pyrshah.  

| Ka '''argument''' ba lai ka dei ka '''query sequence.''' jong phi

| Ka input na ka bynta ka '''query sequence''' ka lah ban long ha ka rukom jong ka '''GI''' number lane ka '''FASTA''' file. Lane, ka lah ruh ban long ka '''sequence record object'''.

| Ka '''GI number''' ka dei na ka bynta ka '''nucleotide sequence''' jong ka '''insulin'''  

| Ka '''qblast function''' ka shim ruh ia kiwei ki jait option argument ba bun.

| Kine ki arguments ki long kiba syrïem ha ki parameters bapher bapher ba phi lah ban buh ha ka '''BLAST''' web page.

| Ka '''qblast function''' kan pynphai ia ka '''BLAST''' results ha ka '''xml''' format.

| Phai biang sha ka '''terminal'''.  

| Ngi dei ban pyndonkam da ka '''Blast''' program, ba tikna.

| ka shong ruh lada ka query sequence jong ngi ka dei ka '''nucleotide''' lane '''protein sequence'''.

| Namar ka query jong ngi ka dei ka '''nucleotide''', ngin pyndonkam ka '''blastn '''program bad  "nt" ka thew ia ka '''nucleotide''' database.

| Ki jingtip ba kham bniahsShaphang kine ki don haka '''NCBI BLAST''' webpage.

| Ia ka '''blast output''' la buh ha ka variable '''result''', ha ka rukom jong ka '''xml''' file.

| Nion '''Enter'''.

| Ka shong ha ka jingstet jong ka internet jong phi, ka lah ban shim katto katne minute ban pyndep ïaka '''BLAST''' search.

| Ka long kaba kongsan ban save ia ka '''xml''' file ha ka disk shuwa ban iaid shakhmat.   

| Type ia ki line harum ban'''save''' iaka '''xml file. '''

| Kine ki lines jong ki code kin sa save ia ka jingwad kum '''blast.xml''' ha ka '''home''' folder.

| Phai sha ka '''home''' folder jong phi bad wad ia ka file.  

| Click ha ka file bad check ia ka jingdon jong ka file.  

| Hangne u don u code, lada phi kwah ban pyndonkam ia ka '''sequence record object''' na ka '''FASTA''' file kum ka query.  

| To ngin ia phai biang sha ka '''terminal'''.  

| Ka bynta ba bud ka dei ban '''parse'''  ia ka file ban '''extract''' data.   

| Ka synjam ba nyngkong jong ka parsing ka dei ban plie ia ka '''xml''' file na ka bynta ka input.  

| Type kumne harum ha ka prompt. Nion '''Enter'''.

| Kaba bud, '''import''' ia ka module '''NCBIXML''' na "Bio.Blast" '''package'''.

| Nion '''Enter'''.

| Type ia ki lines harum ban '''parse''' ia ka '''Blast''' output.

| Ka BLAST '''record''' ka don ia baroh ki jingpyntip ba phi kwah ban '''extract''' na ka '''BLAST''' output.

| To ngin ia print khyndiat ia ki jingpyntip shaphang baroh ki '''hit'''s  ha ki  '''blast report''' jong ngi kiba kham heh ban ha ki jaka ba ki mih.

| Type ia u code harum.

| Na bynta ka '''match''' ba kan long kaba tikna, ka expect '''score''' kam dei ban duna ia ka 0.01.

| Ngin ia print ruh ia u '''string'''s uba don ia ka '''query''', ka database sequence ba la pynbeit bad u string ba pyntikna ia ka jingiadei bad jingbymiadei ki positions.  

| Nion ia u '''Enter''' key arsien ban ioh ia ka output.  

| Khmih thuh ia ka output.

| Na ka bynta kawei pa kawei ka alignment, ngi don '''length, score, gaps, evalue''' bad '''strings'''.

| Phi lah ban ioh ia ki jingpyntip ba donkam da kaba pyndonkam kiwei ki '''functions''',  ki ba don ha  '''Bio.Blast''' package.

| Ngi lah poi sha kaba kut jong kane ka tutorial.

| To ngin batai lyngkot. Ha kane ka tutorial, ngi la pule kumno ban run ia ka '''BLAST''' na ka bynta ka query nucleotide sequence da kaba pyndonkam da u '''GI''' number.

 

| Bad, ban parse ia u '''BLAST''' output da kaba pyndonkam da ka '''Bio.Blast.Record''' module.

| Na ka bynta ka assignment, run ''' BLAST Search''' na ka bynta ka '''protein''' sequence kaba phi kwah.  

| '''Save''' ia ka output file bad parse ia ka data kaba don ha ka file.

|Ka assignment ba lah dep jong phi ka dei ban don ia ki lain jong ki code ba harum, kumba lah pyni ha kane ka file.

| Khmih thuh ia u code. Namar ka '''query''' jong ngi ka dei '''protein''' sequence, ngi lah pyndonkam '''blastp '''program bad "nr", kata ka mut, ka protein database ka bym da donkam na ka bynta ka '''BLAST''' search.

| Ka video kaba don ha ka link harum ka batai lyngkot shaphang ka Spoken Tutorial project.

| Sngewbha download bad peit ia ka.

| Ban tip kham bniah, sngewbha thoh sha ngi.

| Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Sorkar India.

| Khambun ki jingtip halor kane ka mission ka don ha ka link harum.

| ïa kane ka script la pynkylla sha ka Ktien Khasi da u Yuwanki Kharlukhi na Shillong, bad ma nga u Hezekiah Lyngdoh ngan pynkut noh. khublei ba phi la ïasnoh lang..