Question: What further work I can do with BlastP results ?
0
gravatar for guskalja
4 weeks ago by
guskalja10
Göteborg
guskalja10 wrote:

**Hello guys Just before I install blastp (LINUX platform ) and did a tutorial https://angus.readthedocs.io/en/2018/running-command-line-blast.html (to be frank -Copy past the scripts and generated result).

I would like to know " how I can choose the best hits by using scripts or else i have to do it manually? although, what further I can do with data?"

The final results look like this(See below)**

Database: zebrafish.1.protein.faa
           53,088 sequences; 38,547,521 total letters



Query= YP_220550.1 NADH dehydrogenase subunit 1 (mitochondrion) [Mus
musculus domesticus]

Length=318
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  NP_059331.1 NADH dehydrogenase subunit 1 (mitochondrion) [Danio...  426     8e-149


> NP_059331.1 NADH dehydrogenase subunit 1 (mitochondrion) [Danio 
rerio]
Length=324

 Score = 426 bits (1096),  Expect = 8e-149, Method: Compositional matrix adjust.
 Identities = 216/313 (69%), Positives = 263/313 (84%), Gaps = 0/313 (0%)

Query  4    INILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEPMRP  63
            IN L   VP+LIA+AFLTLVERK+LGYMQLRKGPN++GP G+LQ  AD +KLF+KEP+RP
Sbjct  10   INPLAYAVPVLIAVAFLTLVERKVLGYMQLRKGPNVMGPRGLLQSVADGVKLFIKEPIRP  69

Query  64   LTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSGWAS  123
               S  LF+ AP L+L LA+ LW P+PMP+P+++LNLGILFI+A SSL+VYSIL SGWAS
Sbjct  70   SMASPILFLTAPVLALILAMMLWAPMPMPYPVLDLNLGILFIMAISSLAVYSILGSGWAS  129

Query  124  NSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWPMAM  183
            NSKY+L GALRAVAQTISYEV++ +ILLS ++ +G Y+LQT  TTQE  WLLLP WP+A+
Sbjct  130  NSKYALIGALRAVAQTISYEVSLGLILLSAVIFSGGYTLQTFNTTQEDTWLLLPLWPLAI  189

Query  184  MWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTIIFL  243
            MWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFF+AEY+NI+LMN  +T++FL
Sbjct  190  MWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFLAEYSNILLMNTHSTVLFL  249

Query  244  GPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLALCMW  303
            G  +  + PEL + +   +  +LS  FLW+RASYPRFRYDQLMHL+WKNFLP+TL L +W
Sbjct  250  GASFTPDAPELMTISIATKTAMLSILFLWMRASYPRFRYDQLMHLIWKNFLPITLVLVLW  309

Query  304  HISLPIFTAGVPP  316
            HI+LPI  AG+PP
Sbjct  310  HIALPIALAGLPP  322
alignment • 158 views
ADD COMMENTlink modified 4 weeks ago by genomax62k • written 4 weeks ago by guskalja10

Well, what do you want to know about these sequences?

You obviously ran them through BlastP for a reason, so there must be some question you’re trying to answer by doing so? What you do with these results next is entirely down to the question.

ADD REPLYlink written 4 weeks ago by jrj.healey10k

I am new to bioinformatics, To be frank. Example: Okay, i have the results which see in the top of this page. If I want to copy first 100 similar hits. What script or command, I can use for coping? - My blast result | Copy first 100 hits >newfile !... what scripts can I use for this?

ADD REPLYlink written 20 days ago by guskalja10

If I want to copy first 100 similar hits.

You seem to have captured just the top hit though in example above.

ADD REPLYlink written 20 days ago by genomax62k

Please add the exact blastp comand you used in your post above. The answer to your question will depend on what output formats you chose etc.

ADD REPLYlink written 20 days ago by jrj.healey10k

Are you doing this to learn on your own or is this an assignment question?

ADD REPLYlink written 4 weeks ago by genomax62k

I am learning own(Definitely it's not my assignment question). I like to perform BlastP Linus platform rather than with normal web blast.

ADD REPLYlink modified 20 days ago • written 20 days ago by guskalja10
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